Hi nblotske,

This is a very good question. I think using your thumb to mute the low E string is fine, as long as you're still able to hold the chord and have it ring true. So for an A major open chord, I think using the thumb is fine for muting the 6th string.

I don't believe using your thumb to mute the 6th string will slow your progress, but you just have to remember to adjust your grip according to which chord you're playing.

If you play a power chord with a root on the 5th string, you may find it pretty tough to wrap your thumb around to mute the 6th. When playing these chords, I recommend muting the 6th string with the tip of your index finger. Anders has a great lesson on 5th string root note power chords here: https://www.guitartricks.com/lesson.php?input=19399&s_id=1503

Hope that helps!