No. "People with disabilities who use service animals cannot be charged extra fees, isolated from other patrons, or treated less favorably than other patrons." (See ADA business brief link below.) Requiring them to stay in a certain room when other guests are permitted other rooms would be treating the person with a disability less favorably than other patrons.
You can verify this information yourself by calling the U.S. Department of Justice's ADA information line at: 800 - 514 - 0301 (voice)
800 - 514 - 0383 (TTY)