Your best bet is to run Miranda NG in a virtual machine with VirtualBox. You can activate the seemless mode in VirtualBox Windows machine after the installation of the guest additions. At least this gives a half-seemless feeling. Or you could disable some plugins in Miranda NG to make it compatible with Wine. One plugin which has to be disabled is the Modern contact list. It can take some time to figure out which plugins have to be disabled to avoid a crash.
I would love a more native solution as well, but with the current user share it's understandable that this isn't a high priority at all. There are also other building sites which are in need of some development love, like some Jabber protocol enhancements. As Miranda NG seems to beat nearly all Jabber clients for Windows or computers in general, I would love to see if some improvements will happen in the future. But I guess this won't happen very soon as well.