I doubt Siddig would have been as upset if it weren't a really dumb twist, or if it made any sense with his established character.
If anything it undermined the most likable things about him. He didn't achieve his successes because of dedication and hard work, he was another souped up Star Trek whiz kid. He didn't botch his pre ganglionic nerve because of his self sabotaging insecurities, he did it to throw people off the track. That took awesome things about Bashir and made them lame. It was a really, really bad twist.