As someone who has a bit of experience in the alt heavy usage of priests now I could give you my two cents.
I feel that if you want to encourage group gameplay you might want to consider alts may not be the problem, I played eve online for quite a while in a group of about 50 real people with an average of 3 accounts each. There were group goals which could only be achieved with having more than could reasonably be multibox, and there were benefits for everyone to being in a group. An alternative here would be to look at making more cooperative content that allows people to work together, is difficult enough to make multi accounting harder (you won't make it impossible but that is ok) and rewards the group. That style of content is probably difficult to do in wurm's setting given the vast difference between a low and high skill player but that might be a different topic.
As far as the idea of smaller losses that can be recouped, when enchanting you want to both have enough favor for things like life transfer and also keep you enchanting bonuses maxed, one of which is 100 faith, I don't think anyone would be too keen on messing around with getting their faith back to 100 when they next want to cast.
As far as access to skills I think you are aiming a little too thematically and not pragmatically, the most popular priest playstyle seems to be enchanters on the pve servers so it would be good to support that across the board. You could go down the route of allowing them to grind their saccing bonus skill but I think this is a flawed idea since locksmithing can't be done with imping, yoyos have 2 contributing skills, butchering isn't an imping skill and cloth tailoring is left as the only one this addresses. I'd say you'd potentially be better off making sure that there is an equivalent skill for each of them. You could go down the route of adding an imping route to a couple of skills or shifting bonuses around or give them all access to ropemaking (and probably farming too).
The next area where alts are significantly useful is in sermons and linking for priests, if you wanted to reduce alts I'd suggest making it significantly easier to hit 100 faith. As for links you'd probably have to completely rework channelling skill gain or remove skill gain when linked since the best way I know of to grind channelling pretty much requires links for maximum efficiency.