As far as Allison Mack's likeness goes, comics and other media have been side stepping that issue for decades. One of the biggest examples is The Real Ghostbusters
which changed the character appearances to sidestep likeness rights disputes (mostly from Bill Murray if I remember correctly).
But has it been conclusively stated by official sources that Allison Mack is the problem? I would have thought DC is avoiding the issue because Chloe Sullivan is a creation of Miles Millar and Alfred Gough. If DC was to fully insert Chloe into the Superman mythos, then they would be stuck paying those guys extra for every appearance the character makes in any media from then forward. There's no way around it in the modern creator's rights culture, and the bean counters at DC probably don't want to even start an expense like that when they don't feel they have to (especially given the battles they've already got with things like Superboy).