Yes. I was aware of that work around and have been thinking about that from the beginning. I could just append a random number on the end of the seconds as well, that's not far from what you propose. I guess my thought is that is a pretty rough workaround for a standard function that Linux has (time) and that the Yun (for whatever reason) doesn't implement. With that said...plus, Yun has the "added advantage" of being able to use the bridge and execute linux functions to get said timestamp.
I think the inability to get fractions od seconds from the Linux processor is a bug. Is there a place where one can do a bug report for the Yun in the hopes that it can get resolved on the next release?