I personally feel that the proposed changes are a bit too extreme, and will have a detrimental impact not only upon PvP, but also upon player's enjoyment of the game. Realism isn't a justified reason for the harshness of the proposed changes; people tend to play these games for authenticity, not realism.
If you want to change the crew system, then you should start slowly to see what impact it has. I propose the following.
1) Have two types of crew, "trained" and "untrained". Untrained crew should offer % penalty, depending on how large a portion of the crew is untrained.
2) Crew in open water is persistent.
3) Crew regenerates in the open water. Regenerated crew are untrained. Regeneration could be approximately 5%/minute in the open water. Regeneration is slowed by amount of days at sea.
4) When in a port, players may pay a fee to fully replenish their crew levels with either trained/untrained crew. Price should be automatically adjusted depending on amount of crew missing and untrained/trained crew to replace; trained crew, should naturally cost more.