The Jedi don't have many abilities which directly cause death in the same way that Force Lightning does, but Jedi can of course use the Force to indirectly cause death in a multitude of ways:
While the Jedi do not have Force Lightning they can use a version of Force Choke, which is after all just a form of telekinesis. Luke demonstrates it on Jabba's Gamorrean guards in Return of the Jedi:
Luke did not kill those guards because he didn't want/need to, but there's no reason why he couldn't choke them long enough to kill them if he wanted to. Since Luke could do it I see no reason why Yoda (or any other reasonably powerful Jedi) wouldn't be able to.
Yoda could theoretically have dealt a lethal blow to Palpatine even after he'd lost his lightsaber, either directly (by choking Palpatine) or indirectly (deflect Palpatine's Force Lightning, crush him with a heavy object, etc.). However, it's very unlikely that Yoda would have succeeded in dealing such a blow before being killed himself, which is why Yoda retreated.
There are definitely examples of Jedi using Force abilities that are directly lethal in Legends. For example, the Jedi have a version of Force Lightning which they call "Electric Judgment":
(Apparently a change in the name of the ability is all that's needed to make it all good for the Jedi.)
In Legends, Mace Windu gave General Grievous his cough by crushing Grievous' lungs. Windu probably would have been able to kill Grievous with this technique alone if Grievous hadn't managed to escape in a gunship.
The additional light side Force abilities from Legends means that Yoda would have had more direct Force abilities to use against Palpatine ("Electric Judgment", a more powerful crush), but it's still unlikely that Yoda would have prevailed. After all, Force Lightning is one of Palpatine's favorite abilities so he uses it much more often that Yoda would have used "Electric Judgment" or similar. Fighting fire with fire is not such a good idea when your opponent is a pyrotechnician.