On the contrary, I think it'd be received well. The problem with Baker to McCoy is that Baker had a lame ending and it wasn't even Colin Baker playing him. In this case there'd be a McGann adventure and then he'd regenerate at the end. You wouldn't even need to put Eccleston in there if there was an issue. Just end with the regeneration.
Well, yes, that's just my point. If you end it honestly with McGann just beginning his regeneration, a la "The War Games," that could work fine; but if you paste in stock footage of Eccleston and pretend he was involved when he really wasn't, that would be seen by a lot of fans as a cheap trick, just like putting McCoy in a wig and pretending he was Baker was a cheap trick.
Though I think maybe it's best if the mystery of the Time War is preserved. I'd like to see a season of McGann having normal Doctor-style adventures and then end with him just heading off to begin fighting the Time War, and letting that be the last we see of him. The Doctor went to such a dark place during the War itself that I don't think I'd really want to see it. It wouldn't really be Doctor Who
, any more than watching the Doctor sulk in a 13th-century monastery for a whole season would've been. Better to just show the before and after of those anomalous periods and focus the show itself on the times when he's wandering the cosmos having adventures with companions by his side.