I like the perspective in image 4. Interesting how different churches are and the lighting. The Cathedral I just did has a lot of yellow where your's blue.
As far as the noise, how many brackets did you do? Looks like you maybe you did not have enough to get all the detail in the shadows. The other thing to help noise is make sure you have your photomatix box set to reduce noise on ALL under exposed images. The other thing in your camera make sure you have the NR turned on for long exposures. IF you have not had these few things done it should help you moving forward.
In photomatix what I have learned is in low light situations you need to use the shadow slider, shadow clipping. Also the luminance needs to be dropped down in and gamma can be pushed up to compinsate. The next is the lighting slider. The more to the right will help reduce noise in low light as well but it does alter your lighting source, Sometimes it looks cool though. I have done a lot of low light shots and these are all things that have helped me. NEVER use the photomatix presets. Knowing what the sliders do and how they function in different lighting situations will help with your processing. Few last things would be to use noise reduction software like noise ninja or topaz denoize and bring in your original exposures and mask in the noise areas.
One thing is many people do not use masking as much as they should and alter/adjust their original exposure to help the tonemapped version. When I process I always use the original files (MOST all of the time) to add in and take out detail. I do not want to come off snobby to anyone in this forum (because everyone who try's to do HDR deserves a pat on the back because it really is not as easy as many think) however photomatix takes you sometimes 50-80% where you need to be, photo shop and filters finish up the job but, there is truly another level of processing that one can do to really complete the image and thats where masking comes into play.
The sky as Bynx said could also easily be fixed by masking..Sometimes that Highlight Smoothing creates blown out spots or banding in certain situations if you crank it to far to the right. I have never used that Highlight Smoothing slider all the way to right and see it make such a huge difference that did not compromise somewhere else. It does help but at some point it does worse than good. There is a balance though... if you choose to use the Highlight Smoothing slider then adjust the white point slider and strength to help prevent those problem areas I just mentioned. Perhaps Bynx keeps those sliders down so it does not effect his processing as much. I like to keep my strength pumped up as much as possible when possible but, thats my style.
sorry to go on and on I just am here to offer as much help as I can. lend another eye. We all have different methods of processing so soak it all in like a sponge.....
Cheers and good night!!