Well, if you are ripping the old EEPROM out then you can use any programming language you like, since you'll only have compiled code on the chip. Frankly this sounds likely to be a complete waste of time, because it is so difficult to write code for a computer that has something like 60 I/O lines, many of which are timing dependent.
For what it's worth the code for our strategy chip is written in C++, and the calibration (the variables used to tune the car) are stored on a separate chip, so when we go into production we use EEPROMs for that one until we're happy that the cal is good.
If, on the other hand, you wanted to write a basic engine management system for a race car from scratch (ie with no emissions to worry about), it is a lot simpler since in theory you only need timing mark and air mass flow rate as inputs, and you could add a throttle position sensor, and air temperature and coolant temperature if you want.
Cheers
Greg Locock