The Sheppard site is inherited from the original Sheppard East LRT plans, and if I am not mistaken, the land has been purchaced and reserved for transit.
The Zoo is a highly seasonal destination, very busy on Summer weekends but not busy at all during the cold half of the year. However, if the LRT tracks go to Sheppard and Conlins anyway to reach the MSF, then perhaps it is not a bad idea to extend a bit further and get a branch that serves the Zoo.
One strange side effect of the better transit to the Zoo is that the latter will lose quite a bit in parking revenues. Probably will happen anyway when the Sheppard / McCowan subway station opens (+ express bus from there to the Zoo), but even moreso with the LRT link. Not that fewer parked cars is a bad thing, but the city has to keep in mind that the subsidy that the Zoo is getting might have to be increased once the transit gets better.