David,
Run a recent version of IOS 15.1.4M train perhaps.
There should not be a problem with IPsec over L2TP link for control plane, dataplane might however suffer due to added overhead - i.e. try avoiding fragmenttion :-)
L2TP is a layer 2 datapath technology, it should be transparent to L3 and above (where IPsec sits).
What's the config you are spepareing for l2tp? Dialer based?
M.