Ok then i will probobly go with the SD Solution. Sorry to ask but what do you mean with "under fill"?I wouldn't risk it. You also have components on the other side of the board, which could fall of and a new eMMC isn't as cheap as an SD either. Maybe it even has under fill and then it could get really nasty.
You can leave the old eMMC in the system, if the clk signal is capped an ideally grounded on the eMMC side the eMMC won't do anything. You could also remove the 4 resistors if you don't want to cut the clk trace, then the eMMC would be seperated from all the data signal lines.
If i have to choose i will probably take a full size SD Card. Or do you think that MicroSD cards are faster because they are more optimized for devices like smartphones for loading apps from them?
Also, i saw that in the other thread you mentioned to put 30Ω Resistors into some lines, is this necessary? And you also put a capacitor between two contacts.