Which makes me wonder how other servers are managing to run it without an issue.
Speaking personally, we're not, but we've mitigated the issues. We've stayed on MCPC Bukkit #83 and IC2 1.95b. In this older setup, secondary worlds suffer from loss of orientation etc. only when the client unloads a chunk, which means you can (for example) carry out a mining operation in a mining world using IC2 machines. This only works for us because our secondary worlds are "temporary", reset every 6-8 weeks or so. It wouldn't be a solution if you have a series of permanent worlds and wanted to have permanent IC2 installations in them.
When 1.3 comes and if these issues still haven't been resolved, we'll be making a choice between dropping the multiverse or dropping IC2. At the moment I'm inclined towards the latter, mostly because of feature bloat and many many bugs in the vanilla version, not especially because of this issue, although it is a factor.
It's not an issue for some servers because they don't have multiple worlds, simples. Although having a temporary mining world is extremely common, especially if you've limited the size of the primary world eg. with WorldBorder.