I haven't been at this very long, but share the same concerns. Here are my thoughts on prevention:
1. Stabilize, eliminates moisture uptake and eliminates cracking risk. But stabilizing some woods is impractical or impossible. These woods require special care, like ebony, snakewood, etc.
2. Less heat while drilling. This is a common recommendation when working with Ebony, snakewood, or buffalo horn. Drill slow, clean and cool the bit with denatured alcohol.
3. Seal the drilled hole with thin CA and then carefully re-drill the excess. Also seal the end of the flush trimmed blank with CA. This will slow moisture swings.
4. Use a more flexible finish. I used BSI thin for a long time, but it seems to be brittle. Recently switched to Mercury flex based on reviews, not enough experience with it to comment on cracking. I also considered BSI gold, which also has good reviews. Medium CA will be more flexible than thin (in general).
5. Obviously proper care on the finished pen is necessary. Hank has this covered quite thoroughly in his post.
6. Start with wood that is close to equilibrium MC of the ambient condition of the pen. A pen that is made at EMC in South Florida will probably crack if it is sent to Arizona. There are threads about this specific concern. Store unstabilized blanks indoors, climate controlled area.