Dear Rabbi, I have attended many smachot which were held in the catering hall of a conservative synagogue. When it came time to daven mincha or maariv, which were not directly part of the simcha. The minyan is held in a crowded hallway, a public area, or even in the hallway outside the bathrooms. This is done rather than dasven in the same room as a kosher sefer torah in an aron kodesh. I don't understand the basic philosophy. does this not amount to insulting the sefri torah in the aron. The minyan was completely orthodox. I find it personally very insulting to the aron kodesh and the sifrei torahs it holds.
I understand your perplexity on this issue. I will try to explain the other side. Since a mechitza seperating men from women is a basic facet of a beit knesset according to halacha, placing a sefer Torah in a shul where there is no mechita does not imbue the place with the sanctity of a synagogue. It might be argued that making the synagogue without a mechitza is the "insult" to the sefer. Not dovening there might be seen as an attempt not to compound the insult. Rabbi Soloveitchik ztz"l was quite stringent concerning the prohibition of participating in a service that is mixed (men and women). Though the present service is seperate, dovening in the place of such minyanim could be seen as approval. I think it is important generally to not do things that reek of self righteousness, while at the same time attempting not to break clear halachic directives. I would ask the local orthodox Rabbi if he considers it an aveira to hold a seperate minyan in a conservative shul, and act accordingly.