I’d put aside the words “Villain” or “Bad Guy” and focus on antagonist. That’s a person who has good reasons for what they’re doing, they just aren’t willing to compromise with another group of people about what they both want. This kind of character is much loved by the Empire game runners as they’ll generate game all by themselves by grabbing hold of plot and refusing to compromise for “The Greater Good”. For this they will be villified as unmutual and “wrong 'uns” but stand fast as you make great game .
Last time I played someone like this I put myself very much in the mindset that he was a patriot doing what he did to protect his people from outside aggression. Yes some people might have died in the name of progress but well you can’t make weapons of mass destruction without breaking some eggs and all that. Just keep in mind that you’re the hero here and people who disagree with you are the selfish no-goodniks. It’s all about a healthy sense of self belief, which handily the Virtues entirely support. Just pick a virtue or two and go hard, possibly with the aid of hallowings, annointings, other auras or even tonics to push aside any pesky second thoughts.
The other thing to do is have a self supporting world-view and reasons for why you do what you do. As a Highborn you will have an entirely justifiable suspicion of the eternals and their toxic effect on the Empire. So worrying about how that’s going to effect the souls of the lineaged is the right and virtuous thing to do. Other people might be negligent but you will shoulder the burden of protecting the rest of the Empire from the threats they don’t see.
And again don’t think of disney villains, think like Cardinal Richelieu villain to some, but he and many would consider him a patriot who helped create France and indeed the idea of the modern centralised state.
Highborn Synod Priests are the politicians of the nation and as with most things if you’re in power (which you need to be able to get shit done) someone else isn’t. Even just playing a politician and playing the political “game” will cast you as a villain to some, you won’t even need to twiddle your mustache, unless you want to :).