NathanKell posted info a nice hidden treat that should fixe this behaviour on the KSP subreddit. There's no GUI setting for this so it would have to be set by editing the file directly. I'm not sure whether this also fixes it for non-command pods, I will check tonight.
[–]NathanKellRSS Dev 12 points 3 hours ago
The switch of control point when going IVA can be turned off in settings.cfg. Change IVA_RESETS_CONTROL_POINT from True to False.
I added that in 1.0.5.
