Your alignment doesnt influence the ending at all.
Only thing that determines if you become a good god or an evil one is how you handle the dialogues with the Solar after each Bhaalspawn kill. Generally, if you took mostly "evil,selfish,greedy" answers, then you will be evil. You basically have 3 options for a god:
1.Really, really good, the solar will praise you and says she will fight with you(good god end)
2.Kinda good, the solar will tell you it is yet to be determined if you have overcome the taint(good god end)
3.Evil, solar tells you how much she despises you and that your time as a power will be a hard one(evil god end)
If the PPevilchoices is set to something greater than 3 (and less than 6), you will become an evil god, to speak in game mechanic terms
.