While I agree that some mechanics can possibly be changed, adjusted, or added to make losses feel like a more natural part of gameplay, a big part of this does come down to how the player wants to play. The way I see it, it's intended that it isn't going to be a matter of IF you'll suffer losses or crushing defeats, it's just when. The important part in insuring that this doesn't take the fun out of things is the player will still feel like they've made some form of progress.
Some players just refuse to accept loss. There isn't anything you can do about that. If you play smart, this can be minimized. Especially if you have some extra ships mothballed at the storage facility. Maybe there should be a way for players to "hitch a ride" back there rather than the current respawn mechanism. Heck, I suffered a miserable defeat recently after making a navigational error that put me in contact with a large pirate fleet while I was at critically low CR from running out of supplies partway through a journey. I took the hit, limped away in a frigate, and re-kitted.
Experience was still gained, but there needs to be something a little more. A feeling of personal, permanent progress even in the face of defeat. In DF, you might have 3 survivors, low supplies, and a cloud of miasma after a defeat, but you've still got what you built. Pilgrims will comes.
Maybe a mechanic that allows slow recovery of your flagship if destroyed in battle. Your fleets pride is destroyed in an engagement gone wrong, but you've got a few spare creds and can hire an independent force to tow the hulk back home for repairs and refitting. It could appear in your station at 1% hull and 0% CR, with most of the weapons stripped.