Old question, but: while this is not possible in urxvt, I made some changes that will add an option (secondaryWheel) to do exactly that, and make it behave like VTE-based terminals.
What this new option does, is pretty simple: when using the mouse wheel, if you’re on secondary screen(*) then no scrolling will occur, and instead 3 “fake” keystrokes will be sent to the running application. So, a wheel up will have the same result as pressing the Up key three times, and wheel down will do the same as pressing 3 times the Down key.
(*) not sure whether this is the “official” term or not, but at least that’s how it’s called in urxvt.
Easy enough, but that does the trick: now when running
less or any other application that uses the secondary screen, you can use the mouse wheel to move around (or whatever said application would do, if you pressed the Up/Down keys).
It should be noted that I'm not sure this is actually how things are done in VTE-based terminals - I never checked - but this does the job, so it works for me.
A little more info, and links to the code & PKGBUILD for Arch Linux can be found there:
Hopefully this can be helpful to some!