This is another instance of "asking the wrong question". After completing a flash point, you can simply click on "Exit Instance" (it appears directly above your minimap) to be teleported out - no need to taste death.
That said, your primary question was worth investigating anyway.
I initially did not know the answer to this, so I made a new character to test it.
The face of Gaming.SE
Characters start out with boots, pants, and chest items. These all started with full durability.
I immediately stowed the boots in my pack, and went off to make some friends. Friends who wanted to shoot me.
Thus acquainted, I took stock of my boots and my slacks.
Taking off my boots had spared them from a grisly fate! Huzzah!
So from this, I can state with certainty: if you're trying to corpse-hop from place to place, strip down to your skivvies to save on repair bills.