"as low as possible given the other two settings." If only it were that easy! The problem is that the overall exposure level is also a creative decision. The camera's built-in metering may or may not reflect the photo that you want. It depends on what metering mode you have, what your subject is, how you're framing the photo, whether there's light sources in the photo.... all kinds of stuff.
The "candle-lit church" scenario could be a nightmare. Say you're using center-weighted metering. If there happens to be a candelabra in the center of the frame, the exposure is going to be stopped down by the camera, to compensate for the concentration of light sources in the center of the frame. But the candelabra is probably not the subject, and you probably don't want the candle flames themselves to be perfectly exposed -- you are probably concerned with some other subject, say, people standing to either side. Those people are going to be dark as hell while your candle flames are going to be a beautiful yellow. What you really want is for your candle flames to be on the verge of over-exposed, while your people's faces are nicely illuminated. And guess what? That's fairly easy to do in manual mode. Leave your camera in any mode where it is trying to make decisions for you (including Av and Tv or any Auto-ISO setting) and your exposures will be jumping all over the place.
So set the ISO as high as necessary, and no more. There is a reason for manual mode. It is when the photographer can set take his time and come up with 100% optimal exposure settings for the given lighting. You want faster, you need it automated. Fine. Just accept that there are some trade-offs, that the camera might not always make the same decisions that you would have made. Most photographers do not have trouble setting the ISO and then working within a 1-2 stop range on with aperture and shutter speed controls.
And my point in bringing up film is that you are kind of making a mountain out of a molehill. In my experience (estimating that I have shot about 100,000 frames in the past 5 years) I have found that in most static-lighting environments (even very dark ones) you will be able to work within a 1 stop range 75% of the time, and a 2 stop range 95% of the time. Most of the time, it is not worth it to worry about changing your ISO. Find an ISO that you're comfortable with, and stick with it for a while.
I'll give an example. Say I'm in a dark room photographing people at a party. I've found my "standard exposure" is ISO 1600, f/1.8, 1/50 using a 50mm f/1.4 lens. I should be able to get most of my shots within +/- 1 stop from this exposure. So on the dark end, I might go to f/1.4 and 1/40 (which is pushing things with respect to shutter speed, but I'd rather take my chances with 1/40 and ISO 1600 than get super grainy at ISO 3200), while on the bright end, I might leave aperture at f/1.8 and move the shutter speed up to 1/100. Yes, I would rather have ISO1600,f/1.8,1/100 than ISO800,f/1.8,1/50.