私がではない。あれほど冷酷な魔術師だった男が、敵を助けたという事実こそが不快だった。
The が in 私が is the case particle as a subject marker. 'I did not. / It was not I (who saved my enemy).' It was the 男(=切嗣) that saved his enemy (= me = 言峰), not the other way around, and 言峰 is saying that it was 不快 to him.
Source: http://www26.atwiki.jp/tmranking/pages/51.html
breakdown:
が= 格助詞/case particle
で= 断定の助動詞/assertive auxiliary, or copula
は= 係助詞/binding particle
ない= 形容詞/negative adjective
eg.
「XXがではない」 It's not XX (who does...)
「XXにではない」 It's not to/for XX
「XXのではない」 It's not XX's
「XXとではない」 It's not with XX