I'm going on the assumption that these were 100% earned on biz travel; Pending Company policy; a case could be made that the company owns them and lets the employee use them as he/she sees fit whether it be for free award tickets, upgrades, or other purposes like paying for lounge access. In that case, he/she could give them back to the company rather than give them to the spouse or just never claim them going on the basis that the miles, like all company property belong to the firm. The company just might allow him/her to keep the miles if returned by the employee (a handshake agreement with the boss). since they technically would not be his/her asset then the miles would not have to be pooled with the other assets.
IMHO, there is no way that these should be pooled. He/She should do whatever it takes to not have these included.
BTW, whatever happened to the non-transferability of miles? Does it apply in this case; from the airlines perspective I mean?