FYI, copy and paste from OpenOffice works just fine with Moodle ;=} OO also provides quite a braod range of macros and extensions that your staff may find invaluable once introduced to them.... from tools for creating ePUBs, to tools for blogging, building wikis, creating coursework, etc And use of open software places them in an intellectually stimulating environment committed to such tools and the user community, an aesthetic that Word users are probably unfamiliar with, lol
I am very concerned that you indicated that you did not have success with asciimathml because a) I am very fond of asciimathml, b) I have been working hard with Mauno and others to make its usage as simple as possible, and c) I think we have been pretty successful in making asciimathml useful .....
So, I would if nothing else appreciate you letting us know about the problems you faced with asciimathml as I could not finding that you had posted about it previously. As has been mentioned, using a js based tool allows one to invoke the same parser where ever the resource may be located as you can i) include the js in a stand alone resource, ii) reference the js in a resource where the js is not inside the Moodle, iii) as well as invoke the js via theme which can be differentiated by course, user, category etc.
Additionally, we have been looking at a variety of fallback schemes (mimetex, mathtex, mathtran, WA, google docs and even others.....) and some (for example google docs) promise the advantage of being able to totally dispense with any tex rendering binary on the Moodle server.
Lastly, while I am clearly being dramatic about this, there is a bit of a war going on, and for MathML to continue the MathML using community most grow and be vocal....
Glossary autolinking can be a HUGE headache as things start to grow..... so it may be wise to turn this down now anyway....
I am also worried that you seem surprised that you would need tex filter and filteruploadedfiles turned on. the later simply "enables uploaded files (HTML and text only) to be processed by the filters system" http://docs.moodle.org/en/Filters#Filter_uploaded_files . This means that if you want the display of uploaded files to be subject to the tex filter, you would also need to turn on the Tex filter. It is the combination of the two that adds the tex filter to the screening of uploaded files which normally would not get passed through filters.
On the other hand, if the profs are building these word docs why aren;t they using equation editor as use of equation editor would on conversion of the doc to html render the equations as images (which of course would have to be managed in their image folder. Many institutions provide staff with personal ftp accessible web resources. One solution for you is to have faculty upload their converted Word docs to their own web site, and then use an external link to that.
SLES was shipping with access to both apache and apache2, so double check your versions of apache and make sure you are running the same version, and I would compare your conf files as you may discover that you have MIME type and other diffs as far as default config that you may not have considered. While the manner in which the configuration is handled may be different, and sometimes file locations may be a bit different (see, e.g. the discussion of the directory structure employed using apt-get) apache configuration is controlled via apache..... so a side by side comparison of the files should be illuminating - also double check the OS lang setting to make sure that any settings that apache inherits from the OS are consistent (Suse can have unique default settings as it inherits some aspects via its deutsche heritage)
Also remember that encoding can be troublesome from the server side as well as the client side ;=} Here's the w3c pages on such matters.....
Policy wise, perhaps your college needs to rethink its position on FOSS vs COTSS. Asking you to support Moodle without also supporting use of linux, OpenOffice, etc is intellectually and economically indefensible. Moreover, you will notice immediately that Word documents are typically MUCH larger than the same document in other formats. Recently I demonstrated taking an MS-Word doc of almost a meg, and converting that to an OO doc of almost half the size and then to a pdf, an swf and an ePUB, the process resulting in significantly less storage on the server as estimated across all users, and significantly less bandwidth usage to display as well as providing same in a format that is substantially more open than that of MS Word (anyone can compile xpdf....)