I have thought about this, and I cannot think of a way that LN can work without malleability being removed from Bitcoin
Take a look at this (not just quote, but whole post):
TX1:
0) Pays 3x: (Alice + HA1 after T1) or (Bob after T1 + T2) or (2 of 2 Alice + Bob)
1) Pays x: (HB1 + Alice) or (2 of 2 Alice + Bob)
2) Pays x: (HA1 + Bob) or (2 of 2 Alice + Bob)
3) Pays 3x: (Bob + HB1 after T1) or (Alice after T1 + T2) or (2 of 2 Alice + Bob)
4) Pays Alice's change: (Alice)
5) Pays Bob's change: (Bob)
or at this discussion:
Frankly, I don't understand, how channels of indefinite duration could be created without SegWit or SIGHASH_NOINPUT or another possible patch, which makes txid independent on signatures. Explanation appreciated.