My theory is that when you die and become a Force Spirit, you regain the powers you had when you were at your strongest. Yoda was once extremely strong in the force, but by the time of the prequels he was old and weaker. Perhaps there was a point when Yoda was younger where he was powerful enough to affect the weather.
However, Yoda is not the type who would abuse his powers to kill someone. Doing something like that might throw the Force out of balance and prevent him from becoming a Force Spirit any longer, since only light side force users can become force spirits.
only 4 known Jedi have ever become a force spirit after they die Qui Gon Jinn, Obi Wan, Yoda and Anakin and I doubt that Yoda could manipulate weather when he was alive no matter how strong he was in the Force.
If force users can shoot lightning from their fingertips, it's not that much of a stretch to be able to make it shoot from a cloud. Who knows, maybe Obi-Wan, Anakin, and Qui Gon combined their powers with Yoda to help him make that lighting.
Either way, my main point is that Yoda is unlikely to abuse his powers in the way that the OP describes. Killing someone that can't defend themselves as a Force Spirit would very likely darken you and prevent you from ever becoming a Force Spirit again, since only Jedi can become Force Spirits in the new canon.