You can still do the negotiation quest if you've joined one side or the other, as long as neither side controls 8 of the 9 holds.
From http://www.uesp.net/wiki/Skyrim:Season_Unending
This quest starts early in the concurrent quest, http://www.uesp.net/wiki/Skyrim:The_Fallen, but only if the http://www.uesp.net/wiki/Skyrim:Jarl of http://www.uesp.net/wiki/Skyrim:Whiterun (http://www.uesp.net/wiki/Skyrim:Balgruuf_the_Greater or http://www.uesp.net/wiki/Skyrim:Vignar_Gray-Mane) insists that a truce must be negotiated before allowing http://www.uesp.net/wiki/Skyrim:Dragonsreach to be used to capture a dragon. If either side of the http://www.uesp.net/wiki/Skyrim:Civil_War controls at least eight of the nine holds of Skyrim, a truce can no longer be negotiated, and this quest will not be triggered.