ABC and Miramax do fine under the Disney umbrella, so I'm not worried about "kiddifiying" or the insertion of other Disney-related aspects into the comics. At least, not as a result of Disney being hard-handed about it.
I'd be worried about business bureaucrats getting in the way of good comics, if it wasn't for the fact that Marvel's current comics have all been editorally-mandated slime. Quesada drove the creative force out of Marvel Comics completely, so honestly there's nowhere to go but up in that regard.
The most affect I forsee is Universal losing their Marvel rides in Florida, and Slave Labor Graphics not getting to continue the awesome Gargoyles comics ever.