Essay: Gun Handling
First, a minor preface paragraph or two in order to illustrate the current stance on weapons of the shooting nature.

Fact:

In his newest appearance, Shadow the Hedgehog has the ability to wield Earth-Style Fire Arms. These are not "Space Lasers" that are all globby shaped with spots, or GI Joe's "Photon Cannons" that shoot laser-rays that never actually hit anyone (especially not Cobra). They look and act like guns you find here on Earth. Presumably, they also kill and destroy things in much the same fasion.

Fact II:

Most Grown-ups on Earth wig out as soon as they see an Earth-Style fire-arm.

Why?
Because guns can be dangerous. They were especially invented for killing humans. There are spacific hunting-animals guns, and harpoon guns for fish. BUT your handguns and your uzis and automatic-weapons were expressly meant for getting rid of humans, or for use in protecting yourself from other armed (with anything) people. These are instantly recognizable for what they are. If improperly used, they're quite destructive.
The problem arises when people start beliving that a PICTURE of a gun is the same thing as a real gun. Rediculous, you say? Not exactly. How can they make the connection that if "Little Bobby" sees a gun drawn on a piece of paper, that it will FORCE him to rush out, obtain the nearest actual gun, and start committing murders with it?
That is what they're saying, though. That anyone who plays a violent video game, or sees a violent action take place, will be forced to re-create that action in a copy-cat manner. If you observe violence, it makes you do violent acts as if you have no free will.

"Violent Video Games cause anyone who plays them to become violent"

This is what many politicians and other various grownups would have you believe. But every time you hopped General Hawke (GI Joe) across your carpet, did he inspire you to run down to the local pawn shop, grab a wep and eliminate the entire population of your town because he had a gun in his plastic hand?
Not Likely.
However, no matter what your stance on the above issue is, it is irrelevent.

What's done is done (the game has been made) and everyone will continue to think whatever they want about it (reading articles does not change the mind of a grownup, or probably anyone else for that matter). The problem is, how is anyone in marketing/licensed goods/etc going to HANDLE it?

Now all of a sudden, Shadow has become this massive taboo. Little kids can no longer be allowed to look at him because he has guns. The game will not be rated "E for Everyone". But what about marketing this thing? Who is the audience for it now? Yes, the dark/light theme adds edginess, and may appeal to an older audience, but will it wreck Shadow as we know him now?
"The game will not be rated "E for Everyone"
Venue 1:
Archic Comics. It has already been stated that Archie will simply refuse to handle the Shadow+Guns issue at all. They'll never show him with a fire-arm, and they'll utterly ignore his entire plot. They have STATED IT. Ignoring and mis-interperating game plots is nothing new for Archie Sonic Comics. Unsurprisingly, they can't handle guns. The worst thing that happens in their comics is probably Reggie making Archie spill his milk at lunch. Therefor, perhaps Archie was NOT the ideal venue for Sonic comics. They can't bend or develop with the times. But back in the 1990's when Archie signed on, who knew?
Either way, Archie Sonic Comics seem to be in a decline, as Sonic X and the more plot-filled games influence the current fans, and take hold of new fans. However, archie comics are the only remaining monthly Sonic-Dedicated media.

Venue 2:
Sonic X the TV show. This is structured with the characters, icons, and items from the games. It strives to keep a reasonable continuity while incorporating game elements, including new additions. (Cream the rabbit, for example, was not in existance during Sonic Adventure 1)
But this show is for ANY Sonic fan to watch. Will they be able to incorperate gun use? Are they willing? And, if they do, will anyone out side of Japan ever get to see it? Do they NEED to incorperate the Shadow side story at all?

Anyone in America already knows that guns are edited out of shows left and right. Yu-Gi-Oh had Pegasus's thugs pointing in a threatening manner with their finger, while everyone runs in horror. Entire episodes would be slashed to the floor if Sonic X dared try it.

Venue 3:
General Merchandising. This includes things like shirts, dolls, action figures, posters etc. What are they going to do with him? Merchandise goes off limits to babies when it has guns in it. The newer American Sonic clothing line is sooooo tiny, it can only be worn if you are a baby, in most cases. In England, the "Teenage Mutant Ninja Turtles" were "Teenage Mutant Turtles" because the WORD "Ninja" was TOO VIOLENT. What do you think will happen to guns there?
So what're they gonna do?
Only time will really tell that, but I don't think Sonic Team was really considering what this move with Shadow would bring to all the OTHER non-game elements. As this site proves, non-games are a much, much larger market than anyone may guess. There are hundreds of unique items, and the site is not yet near complete.
Unrelated:
Due to the unusual small size of the Sonic characters some of the guns in the game look super huge or somewhat fake. In a few shots, they were rather 2D.
Beware the Stapler.
Ususally the simplest thing is what ends up occuring. The Sonic community will not fall apart into shambles because of one game. (After all, Sonic Underground didn't tear everything down and it was an affront) Merchandising will continue to be what it is now: Damm near un-find-able in most cases cause no one knows how to market. People will like the game, or call it a gimmicky fluke and keep going. Fans are fans, and Sonic fans tend to be True Blue.

The real questions lie in the media (show/comic/ads) and how they'll handle it, because they will need to. However, it seems to have already served its purpose: Creating a whole lotta contraversy and thus, publicity. Like it or not, you know about it, don't you?