What you're saying totally depends on the department. I don't want to go into details on this because it totally depends on the specialty, the institution, etc etc etc... If the clinical department brings in no revenue anyway and is losing money for every patient it sees (this happens in several at my institution), then they don't mind you doing research as long as you're successful. In this case you'll probably make roughly the same if you're an 100% clinical MD as you would as a PhD in the department anyway. If you're in a wildly profitable specialty, you're going to get dinged. This is why I said it's a total generalization. I know in the field I'm going into you take a tremendous pay cut by doing mostly research at most institutions, and so it's almost impossible to find new young MD 80% or greater researchers.
Edit: I'm going to stick this in before anyone else responds as I've been thinking about it. In the intermediate pay specialties, everyone knows there's a huge pay grade going from PP (highest) to smaller/less prestigious academic institutions to big name academic instituitions (lowest). Why is this? Well there's a reputation factor, but the reality is the biggest name places have the most resources and most other big name faculty and will likely be the most flexible about giving you protected time for research. So while everyone in at the big name academic place is getting paid the same, the pay is lousy compared to the rest of the field regardless. All this and you'll probably work harder and get less vacation with your less pay to boot. So the more you want to just be a clinician, the more sense it makes to get away from the big name academic place where we will likely go to get a 80/20 (if it's even possible).
That being said I'm aware of at least one department with a very obvious pay difference between MDs. In the department with which I'm most familiar, the pay differential comes in the form of bonuses and I think this is an institution wide thing. The yearly bonuses are a very substantial contribution to one's salary, and they're entirely based on RVUs. But this is kind of a moot point because I'm not even sure it's possible to get a position here as an 80/20. I've been laughed at for mentioning 80-90% research as a MD/PhD so many times I don't even bother anymore. Also, your pay is determined by the "track" you're on. Some tracks pay better than others--and of course the ones that pay more have more clinical duty. There's all kinds of games played at this at other institutions. Sure, one other big name place might give you as much protected research time as you want and you're making the same lousy pay as everyone else, but all the routine clinical stuff gets outsourced to a different department. BTW, make no mistake. When I say lousy, in my specialty we're talking about 2-fold pay cuts between comparative institutions where you'd do 100% clinical and even 3-fold compared to private practice. Make no mistake, as far as I can see you have to make tremendous sacrifices to be a MD (or MD/PhD) who does significant research, especially in the current funding environment. Every recent graduate from my lab has gone into private practice or is very discouraged by the academic environment they've seen (except one guy who didn't even do residency), and you'd have be really dense to not figure out why.
Regardless, you're still going to improve your pay quite a bit in most specialties by going into private practice and being 100% MD. The short answer to the op's question is still, yes, expect to take a salary cut by doing the MD/PhD. There are cases where this isn't true of course, but you should expect it. If this doesn't appeal to you, don't go MD/PhD.
Must stop editing this post, most start making Thanksgiving dinner...
