I have written LV programs to talk to PROM programmers. You need to know two basic things: The communications protocol to the programming device and the data format that the programming device can accept. Once you have this information, it should be possible to write the program in LV. I did a quick search on the ATMEGA 128L. It appears to have an RS-232 interface so the communications from LV should not be a problem. The data interface may require some bit manipulation, but LV can be quite versatile in that regard.
There may be some tedious work involved, but I think it is feasible to do what you want.
Lynn