1. Leave Vader as the ultimate anti-jedi, but improve him so that he can't so easily be escaped from. Perhaps he spawns with other inquisition/troopers/etc that instabreak/snare vehicles and/or paralyze/daze the target Jedi so that Vader can approach and destroy the Jedi without the Jedi so easily kiting him or escaping. Perhaps a TIE Bomber does a flyby first and incaps/weakens the Jedi first. Something along those lines. There needs to be something where becoming too brazen/visible pretty much guarentees the Jedi's death, and this system needs to be able to target and eliminate the Jedi (almost) anywhere regardless of available players/bounty hunters. This should be in addition to either perma-TEF or increased player bounty hunters after a certain threshold. In short, if your vis gets high enough to summon Vader, it should be an almost guarenteed death for the Jedi.
2. Keep number of available lives as is to account for the game crashing/being dumb at the worst times and also to give some leeway for non-minmaxed players, but change the ghost timer from real hours to account-hours played. This would make it so that the player must either play as a ghost or on their other characters before they are able to respawn as a Jedi again, as well as limit AFKing the timer since the timer is based on account time instead of being able to alt-tab between characters. Somehow I get the feeling people will be less likely to do obvious things with their Jedi if the penalty for running out of lives is 24 account-playhours before their Jedi can respawn.
The other suggestions are fine, including making it harder to insta-travel to a safe haven from almost anywhere as well as giving Jedi more non-afk avenues to reduce their Visibility.