My advice would be to go ahead and play through the top four strings, since the note on the third string gives the chord its "minor" quality. Omitting it means you're no longer playing a minor chord.
With time, you'll learn to selectively strum even at higher speeds.
If you want to really just try to avoid barring the high B and E strings, try simply let up on your barre a little bit - just enough to take the pressure off those two strings. It's really subtle, but you'll be able to tell the difference after some practice.
