You're in the driving seat. You explain whats happened, what needs doing, what the options are. Be up front and let them decide. Usually you can tell how long a job is going take by the time you've run a few diagonostic tools. I'd have said if you can't nail an infected box using HJT etc, etc in an hour and a bit and it's going to seriously disrupt your schedule, then that conversation takes place and it's a take it from there job.
An updated spywareblaster is a pretty good preventative tool. But you are trusting the owner to regularly update programs that need manually updating.