Hello,

I recently got to the point in the main quest line where the Jarl of Windrun asks me to negotiate peace between the two sides.

I haven't yet picked a side or done any of those quests, will this affect the ability to do that later? (Or would my choosing previously have changed anything?)

Thanks!

No and No.

Negotiating peace now will not prevent you from picking a side later (it's only a temporary truce). If you had picked a side earlier and finished the civil war questline, there might not have been any truce to negotiate.

It's not a peace negotiation at all. It's a negotiation of a temporary truce to lay down the arms until the dragon menace has been dealt with. Once Alduin is out of the way the truce is over and the war is back on.