I don't think it'll be a disaster. I could see them pushing for recognizable characters for marketing reasons, but I'm not sure that's necessarily a bad thing. Probably wouldn't mean much more than a mainstream line and an alternate line running side-by-side. And we already have multiple lines, right?
The idea that they'll force Marvel to Disney-fy everything into cutesy kiddy material is just silly. They haven't done that to any of the other companies they own.
The licensing is probably a bigger issue. Universal might be screwed when their license for the amusement park stuff runs out. Or they might just license DC heroes to replace them. Either way, I don't think the amusement park question means squat for comics.
The companies licensing comics may take the biggest hit. It's quite possible Disney will run their comics through Marvel, because the smaller companies aren't going to be able to offer the kind of money that the Marvel division can. On the other hand, Marvel hasn't shown much interest in licensing Disney comics before. Disney/Marvel might leave it alone, because they don't see that much money in those comics anyway. It's still entirely possible things will go on as they are now, on that end.
Will Disney try to put monthly comics in the large chain and book stores? Maybe. But will the stores want anything to do with them? They certainly aren't going to take them on a non-returnable basis like the direct market does. Trades are already in bookstores, so that wouldn't be a change (though it'd be cool if they showed up in dept stores). Personally, I'm pretty sure the monthlies will stay in the comic shops, just like they are now.
At most we might see a comeback of the "newstand" comic (though probably only a limited selection of material), and I think that could only be a good thing - I'd love to see the Marvel Adventures line appearing in checkout endcaps at my local Kmart & Walmart, next to Archie and Jughead (and I also think making them in a similar chunky, digest-sized format would be a smart move). I don't think even that would severely impact the comic shops, though. In time it might help them, as kids "graduate" to an interest in what else is out there. That's certainly how I found the comic shops years ago.
On the other hand, I think the idea that Disney is going to throw tons of money at comics is a pipe dream. They bought Marvel so they could make money from Marvel, not so they could spend extra money they didn't know what to do with. Pay isn't going to go up - what corporate overlord has ever paid an employee more just because they could? The rates & benefits at Marvel aren't going to go up until the creatives can get a better deal somewhere else and start leaving - maybe not even then, because there are plenty of talented up&comers who would happily step in to take their place.
I think the movies are what Disney is really interested in. That's the big money, the big profit potential, and that's where they'll invest. Marvel is going to be on their own with the comics (other than any trickle-down benefits they get from greater IP visibility), and they better make sure they keep them profitable in their own right.