Ok, I'll state this a bit more confidently... (but I'm still worried I'm missing something).
Any time we're in, say, a stable model category where every object is cofibrant (or stable $\infty$-category), then given an object $X$ and a homotopy push-pull diagram (which I won't draw), involving $A \rightarrow B$, $A \rightarrow C$ and $C, B \rightarrow D$ we get a long exact sequence like
$$
\cdots \rightarrow [D, X] \rightarrow [B, X]\oplus [C, X] \rightarrow [A, X] \rightarrow [\Sigma^{-1} D, X] \rightarrow\cdots
$$
Indeed, we have a homotopy push-pull as above precisely if we have a (co)fiber sequence
$$
A \rightarrow B \oplus C \rightarrow D
$$
where the first map is the difference of the two obvious ones. There's probably a good way to do this without being fancy, but the easiest way I see to do this is in the setting of $\infty$-categories: the pushout and cofiber displayed above both have manifestly the same universal property. (I think I'm using cofibrancy here to say that the coproduct and homotopy coproduct should agree... maybe I don't need this- I'm bad with model categories, someone should correct me.)
Anyway, this must be in one of the obvious references. Adams? Neeman's book on triangulated categories? Something like that.
It's not immediately obvious to me that this specializes to Mayer-Vietoris, but that's me revealing too much of my ignorance. Inclusions of open subsets don't seem to be cofibrations, so why should the usual square we write down be a homotopy pullback/pushout (after taking suspension spectra)?