I don't think that theory holds water. He was clearly a significantly above-average specimen in terms of power and yoma ability. If not for Clare's presence and ability, everyone in the party would have been dead, including the experienced awakened-hunter of the group.

I suspect that the reasoning was indeed something like "these people are operating too close to their limit on a regular basis" ... or perhaps "these people are finding too much out about the organization, and might end up being dangerous at some point soon." Clare's utility as an awakened-killer seems to me to be rather unexpected by all, although she wasn't particularly surprised by it. Even her regular contact in the organization said what, "every age has its heroes, just too bad that you aren't one of them..."