if they don't ask for your most recent job as a referee then don't give it - give ones that you would prefer. As stated before, usually they only ask for facts such as - attendance, sick, time keeping but the biggie is "would you employ this person again" to which they can obviously say no. However, if you get glowing references from past jobs and then a dodgy one from the current job it would explain that the problem seems to be with the latest employer and not your wife.
Why don't you get somebody you know with a business to write to them and ask for a reference as if they are giving your wife a job and see what comes back just to set your mind at rest?