At least 3 of DSN's principal cast required prosthetic make-up Worf, Quark and Odo. That's not counting Dax or Kira who also required make-up. So as you said it was doable I think part of the problem with using the Maquis is that whilst they may disagree with how the UFP handled the peace treaty with the Cardassian's is that they would largely have a similar world view. Chakotay might have been better if he wasn't ex-starfleet
I've thought in the past that more Cardassians should've been on the show. I think at least having one Cardassian on the Voyager crew would've led to some interesting stories and interpersonal conflict. The Cardassian Starfleet officer would be dealing with a lot of bias from the Maquis, some distrust from fellow Starfleet crewmen, and then when you add Seska to the mix, it would be even more combustible.
The Maquis were ironed out too quickly in the show's run, but how would they deal with Romulans or Cardassians without blowing each other to bits? "Birthright pt2" from TNG explored the merging of opposing, mutually antagonistic cultures, but that becomes its own discussion in the TNG forum. The other downside is, as valkyrie013 pointed out, is cost, but I'll expand my €0.0175948's worth on that: Prosthetic' application and removal for so many characters becomes a problem in real life, even in the 1960s. And with people not wrongly wanting more non-humanoid aliens representing beings that don't exist to be shown, CGI is the only viable answer. Until CGI rendering of entities based on an actor wearing a suit with bluetooth on it transmitting data to the 3D rendering engine becomes insanely fast and cheap, the best anyone can do is suspend disbelief and not take the human actor too literally...
For my part, I would have loved to see a Cardassian - or at least a half human - half cardassian - officer on board, preferably in the Senior Crew (we got Seven who a human "raised" by Borg & Torres who was a half human/half klingon and even a hologram so, why not?!). It would have been interested to see others, especailly the former Maquis crew struggles to accept him/her while Janeway/Tuvok and Neelix would have do their best to smooth the atmosphere, especially at the beginning. (no matter what faces - color/form - we have, it is the individual behind who is important). -> I never understand why Torres, who herself suffered the rejection of others when she was younger, was always the one who offered a hard shoulder - even was even cruel sometimes - towards Seven...
Rather than writing her off the ship, just retain Seska. Keep the reveal that she is an undercover Cardassian, but otherwise have her around as a cause of tension (therefore, drama) among the crew. You could have the Starfleet and maquis still join together, but Seska's presence as a Cardassian creates fracturous situations from time to time.
I can, sometimes if people are rejected often enough. Letting others in isn't always easy in the back of the mind there is always the little seed of doubt that at some point they'll reject you too.