Academic writing is as much a system of deferences as a system of references. In fact writing depends for its stability on a great deal of respect for established positions in the literature. That does not, however, mean that there cannot be disagreement.
One simple way to state your disagreement with an established opinion involves the Latin word "pace" (I pronounce it PAH-chai). It means literally "peace to" and is generally used to say "with deference to" or "or with all due respect to". It is therefore also sometimes used to say simply "contrary to the opinion of" but I advise against using to signal important points of dispute. It is a preposition, is generally put in italics, and is normally followed by the name of the person being defered to (less commonly a reference to the position being defered to).
Teppo, over at orgtheory.net, used this preposition as follows:
Note that though 3 of 4 doctors called it something (cf. “social construction”), that nonetheless did not make it so (pace Weick, Latour), as there was an objective reality independent of what they thought.
Blog comments of course do not have to be as well-written as scholarly prose, so I hope Teppo won't mind being edited a bit.
The point of the dispute here is "social constructivism", according to which (according to Teppo) naming something makes it so. The parenthesis here probably means "while I find Weick's and Latour's work insteresting in other respects they are wrong about this naming business". That's the standard sense of "pace", and last I checked Teppo did in fact hold at least Weick in some esteem.
There are really two possible points of respectful disagreement here, though the grammar of Teppo's comment focuses on the first:
Pace Weick and Latour, you don't have a disease just because three out of four doctors call your pain a symptom.
Committed social constructivists might of course take issue with this. They might point out that everything depends on what we mean by "disease", for example. And Weick and Latour should perhaps object to the caricature in any case, but the "pace" lets them know that this is mainly a bit of playful ribbing. In any case, here's the second possible point of dispute:
Pace Weick and Latour, there is an objective reality independent of what the doctors think.
Like "with all due respect", "pace" can of course also be used sarcastically. And if we didn't know anything else about Teppo's intellectual commitments (about which I may also be wrong) we might suspect him of doing so here. Notice that "pace" is being used to attribute a position to Weick and Latour and that this position seems a bit suspect (depending on who you are).
One last thing. The Columbia Guide to Standard American English warns that pace "is an intellectual’s term: make certain that your audience will understand it and won’t think it pretentious; otherwise, use English." This actually also offers a positive suggestion: if your readers are part of an intellectual audience, the word "pace" can signal that you expect them pass lightly over the mentioned disagreement. You do not, in this case, expect criticism of your position to be directed at your view of social constructivism.
You are showing that you know that you are not going to change anyone's mind about it on this occasion. You are therefore also suggesting that nothing depends on whether you or Weick or Latour are right about the ontological effects of naming. Your point about modern medicine would still hold, "peace to the constructivists".