I just don't think having a missile launcher in there is that bad an idea!
plus It's not like I have loads and loads of extra models, or tank or artillery variants or anything.
Its not a bad idea, it just makes the unit more flexible, which is not normally something I consider a good thing with imperial guard. If it works, stick with it. I appreciate not everyone has loads of model options!
I try to keep my mech infantry in their iron coffins, but I tend to have at least half my infantry on foot, as I don't own enough chimeras to give everyone a transport. This is because I usually field around 90 infantry at 1500 points, along with a lot of tanks. You can use chimeras to screen your foot infantry too, giving them a mobile cover to advance.
Defending with your whole army in the back field is not usually a good idea. With two of the three mission types involving objectives, you need mobile troop units. This is what you should ideally be using your chimera for doing.