Chi Girl, That was actually the plan. Keeping the job would mean I'd have to keep certain masculine traits anyway (no long hair, male clothing, because both men and women at the job wear pressed dress shirts, etc). As much as I hate the idea of having to temporarily remain in stealth mode, I think I could do it. I mean I've spent the last 10 years of my life raised in a similar church environment, so as crass as it is to say it, I've become good at hiding my true identity mostly out of self preservation

Sandy, No offense taken. I've been around all types of Christians long enough to know the good from the bad. I suspect my co-workers and boss likely would still be on good terms with me as a person, it's the company whose views are problematic.
Lexi, Here's the thing, maybe I'm just being naive, but I'm pretty sure this job just barely came into existence within the last month or so. It's not so much an existing position that he was suddenly willing to promote me to just to keep me, but rather a new position that just opened up, or will be soon. I say that because there's been a lot of talk prior to this about restructuring the way we communicate with our local churches, as well as the fact that a survey was sent out to all employees regarding a number of restructuring plans within the company including questions about more full time positions being available. Maybe it really was just a ploy to keep me around, but considering I had just finished having a conversation with my boss during the meeting in which he explained that I was pretty much the only member of the management team he could always rely on, I suspect I was on the fast track to the position anyway.
Julia, Sorry for the confusion. Reading my original post I could see how that wouldn't make sense. To clarify, my work does not know that I am gay. If they did I would face termination. I knew that when I took the job, but I needed money at the time, and as screwed up as the companies politics are, I liked my coworkers so I never left. Even if I do take the position, I doubt I would keep it for more than 1.5 or 2 years. I believe I have the mental strength to handle remaining incognito at work for just that time, but once stuff like HRT starts I can't say.
As far as changing quickly, I don't expect that anything would happen so rapidly that I wouldn't be able to hide it. I turn 24 next month, so I'm young, but not a teen. Despite being rather tall, I've never been particularly masculine, at least physically speaking. There are Cis Women at my job who are more hairy than me, and that's before I shave my arms. Probably the biggest changes with HRT I would be worried about giving me away would be breast growth and facial changes. From what I've seen facial changes happen slowly and subtlety enough that I it might go unnoticed. Breasts I'm a bit more worried about because I already have natural A cup breasts even as I've lost weight. I've been that way since puberty, so I worry that my body might naturally be more prone to growing (which is wonderful in the long run, not so great for remaining in stealth mode at work).
Anyway, I feel like the consensus is leaning toward taking the job, which I think might be my most practical option at this point. Worst case scenario I can do as ChiGirl suggested and work until they find out. I mean I'd be facing losing the job either way right.