There should have been more dissent between Starfleet and Maquis but I don't think it was a bad idea to have the Maquis quickly become Starfleet.
It was clear at the time it was in their best interest to get along with the Starfleet crew. Also, even if they disagreed with Janeway's decision I can see some of the Maquis respecting it. The Maquis rebelled to fight against Cardassians stealing their homes. Janeway destroyed the array to stop the Kazon from stealing the Ocampan homes.