Forge : 1.6.4-9.11.1.949
BuildCraft: A-1.6.2-4.1.2

A plug on an iron or a touching pipe does not prevent the iron pipe from having its output faced in that direction. Items will bounce back to the input side.

http://postimg.org/image/eq3thuuxj/
You can see a iron pipe where neither of the two not plugged sides has the output.
Wrenching the output from the top side to the bottom side requires multiple clicks.

It seems to me, that the code for checking if the output side is valid, does not check for plugs.

fluid iron pipes show the same behavior