Some time ago, I believe it was Borticus that added the cooldowns as a quid-pro-quot for a small increase of the droprate of Proto Tech in STFs. That was the deal: the bargain, the tradeoff - we would get a small bump, but there would be a stacking timeout effect on cooldowns upon death.
Well, with the new system, that "bargain" has been broken. It's gone; kaput.
Since we are, essentially assured a "flat rate" now for FAs and STFs, there is no more need of that. Leave the damage penalty, sure. But the timeout needs to go.
PS - Take it out of Fleet actions as well. I mean, WHY is it in "Starbase Incursion"? There's no reason to slow us down...