The faction won't be a problem. Put it this way: it will make your trips to town longer when you need to bank or get new spells which doesn't happen often. But merchants? Bah, there are merchants all over the place who will sell to you and if you need to buy food and drink but are far away from merchants selling you, just ask someone around to do the shopping for you and give them a small commission. The only time it will be an issue is if you want to do certain quests but again, I can only think about a few who provide interesting rewards... which can be replaced by something else...
My take: roll an iksar necro if that's what you want to play and enjoy being a god walking among mortals.
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