Yes, why on earth would you want to do that? If you don't have any home automation, then fine the automation code does nothing, if you don't want telephony then the asterisk module does nothing... there is no advantage to removing these modules.
I suspect that you are actually trying to remove those menus from the interface and have not expressed that well. The answer there is you would have to redesign the skin to remove those scenarios... but I advise you tread carefully there, you will not garner any assistance from a team that has worked so hard getting those pieces into the system, to remove them again for you! You will be told you have not selected the right horse for your course. They have more pressing objectives that actually further the project rather than take it backwards. You can do it, but it is involved and not for the feint hearted.