Yes, most of the E-class models are Diesel.

Yes, the MB center is the largest one in Munich.
I bought my ML here :-).

But this doesn´t conclude in the fact that the SIXT station is big as well.
In fact, all SIXT-MB stations are small one´s and they let deliver their cars from larger stations.
The SIXT station here is just a small SIXT counter and a few parking spaces in the parking ground.

So if you want to have a large selection of different cars, there are better SIXT-stations in Munich.
As you want to be safe getting a MB, your idea is good.
In all larger stations you may have a larger selection, but maybe no MB you want.

In my experience, the most friendly, attentive and most hard-trying MB-SIXT-station is in the Otto-Hahn-Str.
They always offerd me (and friens of mine) great service and sometimes gave amazing upgrades. This is, apart of MUC-airport my favourite SIXT-station in Munich, but this may also be personal subjectivity.