I think it just depends and you need to know your LO.
With my 6 month old, he is an awesome sleeper (thanks to BW!). He normally takes 1.5-2 hour naps. If he wakes early once in awhile (but over 45 min), I just get him up because I KNOW that it is not going to effect his overall good napping. If he sleeps for 2.5-3 hours, I also let him sleep because I KNOW that it is not going to effect his night sleep or cause and early waking.
However, back when I started the BW routine, I had to do trial and error because I didn't know if a long or short nap would effect these things.
I'd say do a little trial and error. Let LO sleep however long she wants, but if it effects the night sleep or causes EW, then don't do it again!
Those 3 hour naps probably won't happen all that often, so I'd take advantage when you get them!