Yes, mouseguns are a BAD first option for any shooter...tough to aim, muzzle control is far more difficult due to more rapid muzzle flip and lighter weight, maintenance is far higher, etc. However in the defensive world, they're practically a must. Not everyone can practically conceal a full-size 1911, hi-power, or other large pistol.
I'm hoping the instructor just said that because some people come in with bigger firearms than they practice with and have some troubles. I've seen people who've never shot before in the CCW class I took try to do their live fire portion with a .357mag they literally picked up from the gun shop the day before....that was simply a fail moment.
Either way, the comment was not appropriate for a SD course.