yes. https://developer.pidgin.im/ticket/8053 "This is possible via the statusbox by selecting 'New status' and then click 'Use a different status for some accounts' or by use of the mystatusbox plugin in the Purple Plugin Pack."
Edit: For me (pidgin 2.10.7 from ubuntu package) this works as follows: click the status bar at the bottom of the friend list -> New Status -> Status: Invisible -> Use a different status for some accounts. Although there seems indeed to be a bug, I can only set it to mostly invisible and check "Different" for the non-invisible ones, not the other way around.
However, note whether there is an invisibility feature in the first place depends on the protocols you are using. See https://developer.pidgin.im/ticket/5828
http://www.madhusudancs.info/invisible
http://www.webupd8.org/2010/02/pidgin-plugin-that-enables-invisible.html
for XMPP (g talk, FB, ...)