If the stormcloaks win the CW will they change their currency or just stick to septims for convenience sake? I only ask because I noticed the septim coin was engraved with the words "the empire is the law" and "the law is sacred". Needless to say it would be embarrassing for die-hard stormcloaks to be trading coins that basically say the empire is sacred

Well... There is Tiber's face on the coins, and were named after Tiber, so yeah they will stick with them. Besides if Dunmer can still use them, Nords could also.

If none of the holds have the resources, specialists, or equipment to consistently mint coinage to the standards of the the septim--whether those standards are metal content or consistent weight or magic mint marks--then it makes some sense to keep using such an established, widely-circulating, and reliable currency, even if it originates with the enemy and has undesirable symbolism.

sure they could make their own currency, will it be worth nothing and be a waste of silver? probably, probably not.