Whats your reasoning for thinking that it can't consider the rigid behaviour?
I haven't used CSI SAFE before admittedly, but from a quick glance it looks capable enough of modelling slabs, footings etc.
I'm basically repeating myself with a bit tacked on but in any case:
1. Model the pilecap using shell/plate elements.
2. Model the piles using beam elements.
3. Model the ground either by springs or using an elastic continuum and apply the appropriate loading. If your supervisor hasnt clarified this/given you a place to start go and see him asap.
Without giving the answer away do a parametric study varying E (or the thickness) for the pilecap e.g. E, 10E, 100E, 1000E while keeping the E for the piles constant. At Epc=1000Epiles its probably "rigid" enough at that point, you'll need to fiddle with your value of E to find the point where the flexural behaviour of the pilecap is no longer sensitive to the value of E).
4. Compare the bending moment distributions for each case and write it all up (i.e. the more flexible the pilecap, the lower the bending moments in the piles.
In fact start even simpler, model a 2D frame and do the same exercise and note how the bending moment distribution changes as the relative stiffness of the beam increases by 10, 100, 1000 etc. I imagine this is the general point of the project.
If you cant work it out/its not in the manual go and chat to your supervisor, although again I'd be surprised if it can't do what I'm suggesting.