Prevent design to power up when updating firmware in flash memory
It would be better to use a Schottky diode for this purpose, but there's another potential issue- the signals that are driving the flash memory will be driving the FPGA inputs with the Vcc approximately zero. My reading of at least this Mach02 datasheet is that this is permissible- and that it will not back feed the Mach02 Vcc. You can verify this by testing. 

Assuming that this is not a problem, a suitable diode might be a 1N5817 or similar SMT part which will typically drop a couple hundred mV. 

I don't see a problem with the pullups. You probably want to have a ceramic bypass capacitor right across the flash power pins. 

Note: You could also implement the reset solution @Nake suggests- you may have to do a bit of work to create a reset input. This would be "cleaner", in my opinion.