I was rather irritated when Disney decided to declare the old Expanded Universe including the various comics non canon or "Legends". (mostly because I don't like Disney's new canon)
But I have to admit that I would be curious to see what the books and comics would be like the decision was made to start over again after Temple of Doom like you suggest.
Still I rather wish the publications would move on into the 40s and 50s like we discussed earlier as it would feel to much like wanting to "play with the old toys again and pretend they are new", even if the Indiana Jones canon/timeline is not as filled like that of Star Wars.
But yeah, I have not real problem with the Marvel comics being declared non canon or be replaced with a new comic series.