Yes, the Mazak controls handle the g-codes just fine. As a matter of fact, I only program mills in g-code and don't use the Mazatrol side, not even for probing, Tool break check, etc. There are some things on the Mazatrol side you may want to use however like tool life, max spindle speed (on the tool), slow tool change, HP limits, etc.
As far as block execution speed,.... Mazatrol is extremely fast. You won't be dissappointed with it in that regards.
A few things to consider... Not sure of what options you're looking into or getting for the machine, but the following are definately worth considering....
2D Shape contour (2D High speed machining software... also called MAZACC 2D)
MAZACC 3D (if you do a lot of 3D machining)
EIA Probing software (if you plan on using a machine probe)
EIA Tool break Check Sub routines ( for G code TBC cycles)
Extended workoffsets and 600 set Macro variables, macro B
Extended tool offsetting
There's a host of other stuff too so really look into this...
Tornado Bore, Spline interpolation, Nurb interpolation, Hi-pressure thru spindle coolant (1000psi), different conveyor setups, spiral interpolation (similar to G12/13 but with capability of 3D, "screw" type apps, full pocketing, etc), then other control options like IC card slots (I think this is standard), Floppy drive, all the different ethernet stuff... etc.
It's just a part..... cutter still goes round and round....