Of course, there are thousands of ways the companies could differ, but let me throw out some possible (though maybe not probable) ways that this could turn into a good thing. I'll assume that we care mainly about the "core" Disney parts having to do with feature animation and the theme parks (I'll put the cruise line in with them). Under Comcast, the Disney core would become more "side" or "supporting" parts of the company, rather than the "core." The other aspects of Disney (e.g. ABC) might end up running better under Comcast, which may be able to use them more effectively than current Disney. So, how could the Comcast takeover be good?
1) Since both core areas will be outside of Comcast's own "core", they may end up being run in a less micromanaged style. That is, they might be run as separate (nearly independent) entities, and given heads who are allowed to pursue quality. My understanding is that they've done something like this with the sports teams (also outside their core area...), but I'm only going off of reading others' reports.
2) For Feature Animation (and the film divisions), Comcast's main interest seems to be as a content supplier. In this sense, their interest _might_ be in getting higher quality output, rather than just the profit margins on the individual projects. In other words, it doesn't really benefit their company as a whole to have just a bunch of junk for content, even if that junk makes good margins on its own (like the direct to video animation). My impression is they want something that provides high quality (think HBO's recent productions) for distribution. With current Disney on the other hand, a (business) case could be made that they needed to get maximum return from their core animaiton unit via lower quality production. Of course, the same argument could have been made for the current company , and this synergy was supposed to be a reason why ABC/Fox Family would fit into current Disney, but I think the impetus was backward. That is, it may work better to treat FA as a support of another industry rather than the other industry (broadcast/cable) being just a distribution channel for FA.
3) For the parks, maybe those in charge will "get it." It's certainly possible that new management would return to some of the core "Disney values" that made the parks great, and away from some of the excessive cost cutting (and, it could also go the other way...).
4) With the debt assumption spread across a larger corporation, the pressure on individual divisions might be somewhat lessened. Several people have talked about theme parks being the cash cow for Disney in the past - there would be less pressure on them to continue to be so in a larger corporation.
5) There's always the chance the core Disney areas could be spun off and left to operate as the Disney of old. It's hard for me to imagine a scenario where this would really happen, though. The theme parks, maybe, but I doubt the Disney core would ever be released on its own, and even if so, it probably couldn't last without being gobbled up by some other company shortly thereafter.
Of course, there are lots of bad scenarios, like treating the Disney core areas as things to be mined rather than nurtured, but I won't go into those...