Why was Magus at war with Guardia?
Solution 1:
This is the answer I found on one of the Chrono Trigger wiki :
His main reasons for starting his war against Guardia were left out in the English version; however, in the Japanese version, he stated his intentions of gaining the power to immensely increase his chances of defeating Lavos. Seeing his strong magic and strange appearance, most people took him to be a Mystic himself.
Unfortunately, as I'm not a Japanese speaker, I can't verify that myself. If someone could find the original text and a translation that would be awesome.