i think it will still be better to seperate the keyboard and guitar effects. this way, you can have more control.
i am not sure which module you will be getting but usually the built-in effects apply to the internal sound only. there are some modules that can take in a external signal and route it through the onboard effects but if you do this, you will sacrifice the number of simultantous effects for your keyboard sound. know what i mean?
i know what you mean, teochm. and i've done it before - on my former triton proX. i played both the synth as a keyboard and the guitar through the on-board effects of the triton simultaneously. it was great fun and the sound was good! minimal tweaking required.
unfortunately, i doubt these things work with all rack modules. the motif racks have no sampling inputs. so you're left only with fantom xr and triton rack options. i know how to do it on the triton, but not on the fantom or motif synths. in fact, unlike the triton, i think the fantom and motif does not have an option to route external analog inputs to the internal insert effects in program/voice mode. although i can't be sure as i've never tried it myself, and will probably never be cos i never get to play on these things in the showrooms long enough to find out. if you know, please let me know.
at the end of the day, i feel such a setup will only have its novelty wear out after some time as it is after all, still a huge hassle to transport and set up. technically speaking it all sounds more convenient, but getting down to it, it really is equally bad.
the best solution i can think of, that is less hassle, is to go software - you can get a laptop with a good soundcard, buy native instruments guitar rig, as well as whathever software synths that you want, and run everything through V-Stack or sonar or cubase etc.
however, if i were in your shoes, for church-playing i'd just scrap everything and separate the synth from the guitar efx. just make things simple. i've pulled off all these high-tech stunts in church before, and at end of the day, i realised, it's all not worth the effort, and doesn't always work out.