As nobody else has seen fit to further investigate the Toothpaste Rebellion, I have done some research. The results are below.
*** What was the Toothpaste Rebellion?
Hard Facts: Directly in the wake of the Toothpaste_Disaster, two full sectors (BBY and CRY) plus fringes of adjacent sectors were engulfed in rioting, looting, and treason on a massive scale. Armed Forces was called upon to quell the disorder, and in the process terminated between 11,401 and 100,000 citizens.
Fairly Hard Facts: During the chaos and confusion, an unidentified citizen wearing INDIGO and INFRARED (Batclone) was involved as a ringleader in the disturbance. He was taken down by the Legion_of_Ultraviolence, though not before providing the hitherto-unorganized mobs with enough direction that the "Toothpaste Riots" were redesignated the "Toothpaste Rebellion".
Not-so-Hard Facts: There were unverifiable reports of an extremely strong GREEN-clearance mutant distributing bottles of Exercise_Pills admidst the Rebellion. The (empty) bottles recovered as evidence for this claim had been crudely re-labelled "Toothpasty_Supplement_#5". (Unusual, since TS#5 is not normally a pill, but I suppose that rioters have never been noted for their critical analysis skills.) There are vague reports indicating that Batclone briefly led a group opposing the Rebellion.
Downright Squishy Facts: The Exercise_Pills supposedly being distributed might, perhaps, have come from the misplaced first shipment out of HLK_sector, unless they didn't. Batclone's outfit bears a certain resemblence to several of the ItemsInQuestion, which bears a passing possibility of maybe not being utterly irrelevant. The Green_Bonnets had nothing to do with the Rebellion, unless some High Programmers are right and they did.
*** What caused the citizens to riot?
The ostensible reason given at the time was the revocation of standard toothpaste rations, including the addictive Toothpasty_Supplement_#5. In reality, a number of factors came into play; while TS#5 is somewhat addictive, its mere absence would not be sufficient to plunge two full sectors into rioting - let alone treasonous rebellion against Friend Computer! Contributing factors included:
Long-term frustration: The denizens of CRY and BBY sectors had been forced to put up with various inconveniences and indignities over the yearcycles: multiple forced relocations, repeated delays on repair of local power plants, occasional replacement of standard rations with "mostly non-toxic pre-owned reactor shielding", and cancellation of all Best_Good_Happy_Sector_Hour reruns.
Sedition: Several ringleaders - including Batclone - had been quietly building up dissent over the several yearcycles prior to the Toothpaste_Disaster. It is noteworthy that the loose network formed by Batclone and the others had no apparent purpose other than organization, and then instigation of a rebellion doomed to failure - unlike most Secret Societies that might organize such a thing.
Short-term anger: During the two monthcycles prior to the Rebellion, residents of CRY and BBY sectors were returning to lodgings fouled by the Codemonkeys. The withholding of Toothpasty_Supplement_#5, to which the citizenry was addicted, also played a role in the critical peaking of anger, as did localized brownouts (due to poorly maintained local generators combined with the grid-wide effects of the Four_Reactor_Foam_Flood).
It is also extremely likely that some sort of malefic Viral_Thought_Patterns were involved in instigating the populace to such treasonous behavior, but hard evidence has not yet come to light on this subject.
*** Who was ultimately reponsible?
Investigations have just confirmed that the Toothpaste Rebellion was deliberately engineered by Armed Forces - more specifically, the HLK_sector experimental facility and a number of related divisions in other sectors. Conditions in CRY and BBY sectors were deliberately manipulated to render the populace increasingly discontent, while Batclone and the other ringleaders - all undercover AF agents - spread their influence. When the inevitable rioting occurred, they used that influence to organize the mobs into something threatening enough that Armed Forces' use of extreme force seemed reasonable. There were several purposes behind this plan: to test a number of experimental weapons in full-scale field conditions; to practice deployment and tactics against a multiple-sector insurrection; and to make a show of Armed Forces' strength. All of these would be eminently reasonable goals if pursued in a duly authorized fashion; apparently, when authorization was not forthcoming, they chose the path of treason.
It is worthwhile noting that their plans seem to have been oriented towards the long-term; there is no evidence that they were behind any of the short-term catalysts for rioting. (Although Make-U-CRY-2 was the one to begin Toothpasty Supplement rationing, and is a member of Armed Forces, it does not necessarily follow that he was a co-conspirator, however guilty he might appear at first glance.)
Whether or not the Armed Forces groups in question were themselves puppets for some other force or organization remains unknown; interrogations of the guilty parties have commenced, and may reveal some answers - both on that subject, and the issue of Make-U's involvement.
References: Batclone, Best_Good_Happy_Sector_Hour, Exercise_Pills, Four_Reactor_Foam_Flood, Green_Bonnets, HLK_sector, ItemsInQuestion, Legion_of_Ultraviolence, Toothpasty_Supplement_#5, Viral_Thought_Patterns