It's not like Y-Wings are exactly hard to kill,
OP said it took 4 turns of ions to walk the Decimator off the board.
Decimator always returns fire, 3 dice attack (or 4 if Range 1, but if you're consistently ionized you will never have a Range 1 shot, so we'll ignore it). We'll even remove the stress so that he can use focus.
Focused 3 dice attack vs 1 evade does 1.88 damage per shot vs shields, 1.97 damage per shot vs hull.
(www.xwingdice.com)
At 3 shields and 5 hull, you can expect one Y-Wing to take just over that many (4.1) shots to kill. So it's quite reasonable to suggest that a pair of Y-Wings are absolutely durable enough to escort a Decimator from the middle of the board to fly off the edge if there's no outside interference, especially under OP's circumstances of no focus.
OP, the primary mistake was taking out Cracken before one of the Y-Wings. If you'd focus-fired one of them first, you'd have eliminated his ability to fully ionize the Decimator in a single turn, and you could have cleared stress and lived longer/fought better.