This is interesting. As a few people have said, they're unlikely to interfere with how Bad Wolf and RTD go about making Who, but I guess they may start pushing for a film again?
Odd how the article kept mentioning His Dark Materials and other shows but not Doctor Who (even if they're not even in pre-production). I like to think this won't effect the creative quality of Doctor Who but the pessimist in me thinks otherwise. Sony has a very bad track record creatively and has only barely managed a successful working relationship with Marvel with Spider-Man.
The sale was already in the air before the DW deal was announced, so it's not something that's going to have come as a surprise to the BBC. Best case scenario is the show gets a bigger budget out of it.
Sony Pictures Television is a sibling to Sony Pictures Motion Picture Group, not a descendant. It's got a pretty decent creative track record, most notably Breaking Bad and The Crown.