No this isn't possible, the prefered way of integrating with Mendix is through webservices. To call a microflow you'd need to be logged in as a certain user and many things are dependant on that, such as security constraints and the user's timezone in date calculations. When calling microflows from a webservice this is handled by the webservice user.
There is of course a Mendix API through which you can call microflows, log in users through code and do all kinds of other things. For this API see http://apidocs.mendix.com/
No, Java is available in the back-end but Mendix is hiding all java stuff at the front-end. That is one of the original reasons to start Mendix.