I'm now implementing this in Amiko Pay. In the implementation, I made a minor change to the concept:

To reduce coin fragmentation, I've put the funds of all locked transactions of a channel into a single output. In case of disagreement, the escrow service calculates how much of the locked amount is sent to which party. To enable the escrow service to do this, the amount of BTC in a microtransaction will be added to its TCD.

The down-side is that only a single escrow service can be used at a time for a micro-transaction channel; this is not considered to be a problem, since both sides have to agree to the choice of escrow service anyway. It is possible to switch to a different escrow service without closing the channel, if both sides agree to the choice of the new escrow service. In case they can not come to an agreement, then it's just a matter of settling the on-going transactions and closing the channel.

Note that this reduction of coin fragmentation is no longer possible once real Ligthning-style HTLCs are used. Also note that this coin fragmentation only really occurs in case of non-cooperating (mis-behaving) neighbors: cooperating neighbors will always settle their micro-transactions.

My major concern is that coin fragmentation leads to a large withdraw transaction and high fees; if the fee becomes high w.r.t. micro-transaction amounts, this could change the incentive-structure.