Unfortunately, there is no mucharen't many local trains from Dushanbe. One of them goes to the Konibodom , but it goes notdoesn't got very straight, and just once a week (and sometimes it just not goesdoesn't go at all).
So all I can suggest you instead of M41 (Pamirs highway) is to go via A372 to Osh, and from there take a car or bus to the Bishkek.
But I can't get any news from this region to define, is if there any troubles or not.