You ask whether
it [is] possible for
microtype to work with OpenType fonts loaded with
The short answer is yes. A longer answer would add that
microtype's functionality under LuaLaTeX isn't as complete as it is under pdfLaTeX. However, the limitations are not caused by the use of OpenType fonts.
The version of
microtype that's currently distributed with TeXLive 2012 and MikTeX 2.9 is still version 2.4. However, a late-beta edition of version 2.5 of the
microtype package, dated 2012-05-23, may be downloaded from http://tlcontrib.metatex.org/cgi-bin/package.cgi/action=view/id=608. This version, when run under LuaLaTeX, still isn't as capable as when it's run under pdfLaTeX, but it comes a lot closer than if you stick with version 2.4.
You ask in a follow-up comment how version 2.5 of
microtype might be installed manually under MikTeX. Do you have a "local" directory set up among the directories that are searched by MikTeX? (Bring up the "Settings" app of MikTeX to find out.) If not, do set up such a directory. Then, you could
make sure that this local directory is topmost in the search order (so that the version of
microtype to be installed by you in the local directory are seen before the "official" but now somewhat obsolete version that's still distributed with MikTeX 2.9);
copy the files of microtype 2.5 beta to subdirectories of the local directory (such as
update MikTeX's filename database; the particulars of this update process will depend on whether or not you installed MikTeX in ordinary mode or admin mode.