Oh, this question was specific to the desktop game (Linux). I guess the browser one can save stuff in the localStorage, but I'm not sure it's worth working on that. But for the PC game it would be useful, especially with longer missions.
You should still be able to pause the game in the binary versions (inc. Linux), by pressing ENTER key to bring the menu up.
But yeah, no real "save game" mid-level, I'm afraid.
Thanks, good to know. :) I'll just plan ahead.