How about,
(l1 ++ l2).groupBy(_._2).mapValues(_.unzip._1.sum).toList.map(_.swap)
Unpacking this a little on the REPL helps to show what's going on,
scala> l1 ++ l2
res0: List[(Int, java.lang.String)] = List((1,a), (3,b), (3,a), (4,c))
scala> res0.groupBy(_._2)
res1: ... = Map(c -> List((4,c)), a -> List((1,a), (3,a)), b -> List((3,b)))
scala> res1.mapValues(_.unzip)
res2: ... = Map(c -> (List(4),List(c)), a -> (List(1, 3),List(a, a)), b -> (List(3),List(b)))
scala> res1.mapValues(_.unzip._1)
res3: ... = Map(c -> List(4), a -> List(1, 3), b -> List(3))
scala> res1.mapValues(_.unzip._1.sum)
res4: ... = Map(c -> 4, a -> 4, b -> 3)
scala> res4.toList
res5: List[(java.lang.String, Int)] = List((c,4), (a,4), (b,3))
scala> res5.map(_.swap)
res6: List[(Int, java.lang.String)] = List((4,c), (4,a), (3,b))