You're right! This really depends on the specifics.
For some lenses, like the Pentax Limited series, but basically small prime lenses in general, a lens-based approach just wouldn't be possible at any price. I don't think Canon offers any prime lenses with IS at a focal length under 100mm, and Nikon's 85mm is their only exception to the same rule. Arguably, image stabilization is less important for wider lenses, but the fact remains: if you want image stabilization in a wide or normal prime — or even a short telephoto — in-body is the only way to pay for it.
So, if that appeals to you, in-body is very much the way to go.
If you're just looking to get the setup you describe — one zoom lens with IS and a prime, and you're done, and if you decide that you don't care about IS for the prime, there's really not much of a difference. Either way you're just buying IS one time, and there are some reasonably-priced entry-level zooms with the feature. Even if you buy two such lenses, the price difference due to other factors might be bigger.
If you're looking for a fast, pro telephoto zoom, the situation is different — but not uncomplicated, because we can't compare apples to apples. Canon's image stabilized pro 70-200mm f/2.8 lens is about $1000 more than the non-IS version, and the Nikon equivalents (there, the non-IS version is 80-200mm) have a comparable price spread. But, Sony's equivalent lens is in the ballpark of the pricier choices, and it's hard to tell if the couple-hundred in savings is due to IS or some other decision. And Pentax doesn't even make 70-200mm lens anymore, instead of focusing on the designed-for-APS-C 50-135mm. So is in-body IS a win here? Hard to say!
So, what I'd suggest is to take a look at How much do lens lineups vary across DSLR platforms? and the answers there, and think about what you expect your total lens system to look like, and think from there.
But — and I can't stress this enough! — you can't really plan until you get your camera and start shooting and discover what you like.
When I decided on a camera brand, I sat down and made a chart of what lenses I would theoretically buy to cover this and that focal range, and plotted out my future purchases. Turns out, I love those tiny prime lenses I mentioned above, of which only one was on my imaginary roadmap. Now that's all I have! (Plus some older Pentax primes and a Lensbaby — also image stabilized.)
And, I value having those primes all stabilized. But if that weren't my thing, it might not be important at all. I have a friend who stretched his budget and immediately started out with the Canon pro-level 24-70mm and 70-200mm f/2.8 lenses (the later with VR), and he's been so happy actually taking photographs that he hasn't once stopped to stress about what other lenses to buy.
