I'm sure that filemaker wouldn't have invested all the time in making an interface for FM12 that has huge overtones of up-to-date web styles, without having a path for eventually updating ALL of the features of the filemaker line.
I'm sure something is on it's way. In the meantime if you have to have a virtual app that mimics filemaker pro, why not just use a virtual filemaker pro client. I know worldcloud offers them: http://www.worldcloud.com/hosting/Virtual-clients.php
Also, have you thought about using compiled executables? Or are you married to the need to have a cloud-distributed system?