Did you ever find a solution to this problem?  Our lab is finding that it is very difficult to recover soluble chromatin from Mnase treated nuclei.  Detergents alone or light sonication alone are not working to separate soluble chromatin from large nuclear debris.

Dear Sean, we have already used the CST's kit which based on enzymatic shearing. Even so, this commercial kits suggest sonication for optimal recovery of chromatin. If you don't sonicate your fixed sample, you can't dissociate membrane, cellular cytoskeleton and chromatin structure. MNase, the enzyme which is used in the kits, can only help fragmentation of chromatin, it doesn't break down cellular barrier.

Dear David, we haven't figured out this point yet, unfortunately! We haven't got a efficient sonication instrument, still. 

Here is a very detailed protocol that uses both sonication and detergent treatment after Mnase treatment to liberate chromatin--it does mention that it was not tested whether sonication was a necessary step, but my opinion, at this point, is that it probably is for the reasons you mention.

https://ethanomics.files.wordpress.com/2011/08/chip_protocol_mnase.pdf