I am a Scholar 50. I have completed up to and including Titan Hard Mode (only coil left!). I do not remember any point where I needed to micro manage my pet, nor any time when it would have been beneficial. The most I do is occasionally place the pet or recall it back to me. (This is easy enough to do as its a single command and you point and click and there she flies).

Note, I don't have any fancy equipment or something special to make up for the lack of micro management. I really think its unnecessary (at least up to Titan, don't know about coil). So I would suggest the following:

If you need to place her somewhere, go ahead (can sometimes be useful/different/fun).

Otherwise, let her be.