A "smart" solution would be pretty tricky to do. I also mask out a lot of sky, including between branches and leaves on trees. I do most of masking Photoshop using actions to semi-automate a few key steps. The two main methods I have for selecting the sky are:
Select > Colour range, using white as the reference colour and values of 20-40 for the range. In some cases this can be applied to the entire image, but rarely to an entire set of images as it doesn't discriminate between white objects and white sky. In those cases I will firstly marquee select the area of sky before running the colour range selection. If there are darker clouds/blue sky as well then I'll set the action to allow input on the colour selection so that I can add the additional areas of non-white sky.
Magic wand selection. This is usually used as an initial step before running a colour range selection when there are light objects with a clear demarcation from the sky (e.g. and angled roof) so that I don't have to be too careful with the marquee selection near these objects.
Once the area to be masked is defined by a selection I have other actions to add/remove the selected areas from the alpha channel of the image. Link all of these to function keys and my workflow uses the mouse and 4 shortcut keys to do the masking.
The problem is not so much that it can't be done, but it's something that will only work in certain situations and usually requires some form of manual QA/ baby sitting.
Perhaps a colour range selection may be a useful addition to the other Photoscan masking tools?