Your faction with any group is determined from the sum of five modifiers: race, deity, class, spell effects, and your history of interactions with the faction.
Of these, you can modify three of them, race with illusions, history by kiling things and doing quests, and spell effects by casting spells.
So to answer your question, maybe. The enchanter class is neutral so there won't be any modifier from that. You will get a positive modifier by being the same race, but your deity could give a negative hit you worship a evil god. This is why the standard deity advice for enchanter is to go agnostic.
If you kill enough things belonging to a certain faction though, you will eventually go KOS. As a chanter you can bump this up a little with faction spells, but not much.
One other thing, city guards, merchants and the banker aren't necessarily on the same faction, so you may be able to kill guards fine, and keep selling to the merchant.
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