Not to mention that the Sinai Peninsula has a large and occasionally restless Bedouin population so the IDF would be faced with a territory larger than Israel proper to have to constantly police and patrol.
Is this really true for the times?
Census of population in the Sinai was less than 50,000 in 1960. It was only after Sinai was returned to Egyptian control after 1980 that the Egyptian government began to heavily settle the area. So while I am not sure of what the population would be during Israeli occupation, my guess would be much less than 100,000.
This isn't exactly large. The growth in population of today - around 600,000 (not counting the canal zone) - I think is because of the growth of non-Bedouin as Egypt built more permanent settlements.
Furthermore, in Israel itself, the Israelis have had the best relations with the bedouin out of all the Arabs. Only fairly recently has it come under strain as the government takes more land away from them in order to promote permanent settlement.
I am not aware of any issues the Israelis had with the bedouin population int he Sinai during their occupation - but that could be my ignorance. But given the huge amount of land available and the sparse population, I don't think the bedouin will have much to complain about. Under Israeli control, the chances for ISIS style radicalism is probably less likely to flourish - it really only started after the Arab Spring. The bedouin will probably have less grievances with the Israelis than they do with Cairo today which was much more aggressive in settling the region than the Israelis would be. The Israelis could only really settle a minor amount next to Israel, leaving the vast majority of land to bedouins. Of course, over a larger amount of time, this would become a greater issue. But I don't see the potential size of an Israeli settler population approaching the levels of the non-bedouin Egyptians, and it is likely to be more restricted in its scope.
A lot depends on how badly Israel manages the relations with the bedouins. Cairo has done a poor job since regaining the peninsula which accounts for the problems today. I don't think the Israelis would do as bad based on the historical treatment of their own bedouin population. if Israel chooses the same pattern of development as Cairo did - turning south Sinai into a tourist zone, neglecting development and services of the area, seizing the desirable coastal land, limited benefits from the gas and oil found on their land, etc. - then they'll have the same trouble as the Egyptians do now. However, I think the Israelis will probably do a better job.
So question the size of the population, its hostility, and therefore the difficulty of Israel to control the region.
It certainly might become a problem for the Israelis, and bad decisions would cause blow back, but that is by no means inevitable or even the most likely scenario.