It's like, "look at all the cool shit you can do with Bitcoin!" Then, wait, they pull the rug out from underneath you. What's the point of having script if 90% of it won't be relayed or accepted into blocks? Unless Eligius mines it, of course.
Security concerns (and possible bugs in the code).
Since Eligius will include non-standard transactions, the main network has to be able to check non-standard transactions anyway
Pools which use the reference client for block generation are less likely to accidentally produce invalid blocks.