Gently scratching at the needle holes with a fingernail will sometimes shake the threads back into place too.
In my experience, as long as you haven't actually broken a thread in the weave, the holes will eventually shift back closed with use and washing.
In place of pins, have you tried the Clover Wonder clips? I love those things, I rarely use pins anymore. Sometimes you still need pins, but often I can get away with using the clips.