Organizations change, especially over the scale of millenia. It's the word of three assassins, two of which were members of the Jedi council and the other a personal liason between the Chancellor and the council, who succeeded in killing him where four other members of the Jedi council had tried and failed. Half the Jedi council committing treason by trying and succeeding to kill the High Chancellor certainly gives credence to the late Chancellor's claim that the Jedi were planning to commit treason.

In addition Palpatine wasn't just pulling the strings using the force, he was a genuinely charismatic and popular politician. That would mean that he would undoubtedly still have had support, especially after the thing he warned against happening came true.

An intense investigation into the Kaminoan cloning facility would (hopefully) show some serious foul play

Of course it would. It would show that the clone army was originally commissioned by who else, a Jedi master and former member of the Jedi Council, half of whom just tried and succeeded in killing the Chancellor.

regarding the brain chip that made them all suddenly turn on the Jedi all at once.

Those don't mean anything, they were an intended part of the clone specifications as designed by the Jedi who commissioned them. The bio-chips ensured that the clones could be compelled to follow orders, after all obedience is important in a soldier.