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Well, both have two domains. Separatists gain two domains, one from their deity's list and one other that isn't. Scroll Scholar, sort of like a subdomain, replaces a first level power from a chosen domain. You would still have both domains you chose from Separatist, though...
I can see the argument for it not being legal, however, since both affect a class feature. RAW you may not be able to, so if this is for PFS I would seek clarification, though I'd like to see an official wording on alter vs remove in archetypes.
At the least, in a game at home I'd see no problem in allowing it. I, as a GM, would see no problem in doing so, it definitely isn't game breaking. And, well, like Sean said, it sounds like an awesome thematic idea!

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I thought about this some more and I really think it comes down to how the GM adjudicate domains and domain powers. Kaine makes a really good point that the first level power of each domain is not changed in any way. You have a first level power from either of your domains to give up whether you are a Separatist or not. The text just isn't specific enough for this example.
The Smite example is perfectly clear. You have the Paladin class, it has an ability called Smite, and the archetypes change the Smite power itself. When you look at the Cleric class though, you have a class ability called Domain, but the domain powers are not listed in that block of text (because there are many). Do you say that all of the domains, spells and powers are part of that block of text? If so then I have to say it's illegal. If you take the domains with powers as their own individual blocks of text, then you could argue the opposite.
I'm inclined to give it a go since it's not an unreasonable combination by any stretch and if the PFS GMs say it's illegal then I will just have to fix my character.

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I am disinclined to ask for a ruling in the PFS forums because this is really a rules question and if I post over there, it's just going to be moved back here. Mike Brock tends to only rule on things that are specific to PFS, such as the setting and adjudicating the campaign rules. The answer to this question would apply to PFS and people's homegames (unless you choose to houserule).