I need to implement a distributed XMPP MuC application on the lines of XEP-0289 minus some of the features, in essence I want to have a bare bones implementation of the plugin, my concern is to address fault-tolerance and as of now I do not want to worry about the performance considerations as specified in 289. I have looked into SleekXmpp as a tool to develop server side plugins, but don't know how comfortable it would be to use it for such an implementation, other options I have looked at are OpenFire , Tigase. I am comfortable with Python/Java and other key features to consider would be good documentation, ease of use etc keeping that in mind I would like to know what would be the preferred path to take for this development. Any guidance will be appreciated.
you should be able to write a MUC component that includes FMUC (or similar). The general way to do this would be to use a library that supports XEP-0114 components (e.g. SleekXMPP (Python), Swiften (C++)) and implement MUC+FMUC through that. You haven't said what your concerns with SleekXMPP are, but it's a fairly well-respected library in the XMPP community, so seems a fair choice (I'd pick Swiften, but I'm biased as one of the authors).
Your second option (patching the server directly) isn't generally the XMPPish way of adding customisations (as it's vendor-specific), but should also work if you can find someone sufficiently familiar with the server code, or if you're willing to become so.
To achieve fault tolerance (assuming you mean resilience to server failures) you'd need to run your XMPP server clustered, and also cluster your FMUC implementation. With that done, the usual XMPP fail-over using SRV records in DNS should ensure other servers retry connections to another host.
On a side note, the next version of FMUC (XEP-0289) will have some of the features of the current revision stripped out, and a number of improvements made based on deployment experience, so if your work is not time-critical, it might be of benefit to you to read that when it's released. I also note that there exists at least one implementation of FMUC already (Isode's M-Link, on which I work), and there is interest from other vendors, so using the standard protocol might benefit you in terms of not re-inventing the wheel.