I don't understand the confusion here. If ATC clear you direct to the IAF and whilst routing there you are cleared for the approach you may descend in accordance with the approach once established on it. However, you are not on the approach until you reach that IAF. Any descent below that FL80 needs a specific ATC clearance. If FL80 is too high to intercept then you need to request lower. The only other way around it (assuming weather permits) is to request a visual approach. Surely it is no different to being cleared for the ILS whilst on an intercept heading and realising that your last cleared alt will be too high to intc the GS. I know plenty will just wind the MCP alt down a coupe of hundred feet to make it work but I think everyone would agree that is not strictly correct.
In the circumstances you have described assuming you needed a lower FL/alt to make the approach work surely you ask for descent or at least clarification of the clearance, and not simply descend the MSA without talking to anyone about it first?