No, not without modifying the wyUpdate source code to filter out the particular executable that you don't want ngened.
Can I ask you why NGEN causes your program to never close? Have you investigated it?
The reason I ask is this sounds like a bug in NGEN. And if it is Microsoft should be notified, rather than implementing a workaround in wyUpdate.
Any chance I can see your source code, or at the very least the executable that's acting up? (If so, send them to wyatt@wyday.com )