Seems we are doing very similar things: https://bitcointalk.org/index.php?topic=1340621.0 (also based upon TierNolan's basic idea but reworked to use CLTV with P2SH so no malleability issues and txs should be considered as "standard" for both Bitcoin and Litecoin now).
CLTV is one of the things I have in mind when I write about extending the trading part of Coincer. 
On the other hand, I'm not going to completely abandon current approach. But maybe you know more than I do about current malleability issues in Bitcoin? Because as far as I (think I) know, there shouldn't be anything that could affect this atomic protocol. With BIP66, all parts of BIP62 should be fixed (except those where the malleability comes from ECDSA signatures, but those aren't relevant here as it's the sender who strives for the txid remaining the same and no one else could be affected).Also if you are doing a GUI then with some very minor tweaks you could get it to work with AT blockchains as well (Qora and Burst) as they have supported ACCT for a long time now.
I'll definitely have a look at both Qora and Burst. :c) Although a GUI has a low priority for me, it still is on my ToDo list and eventually will be implemented.