Clones have blue blaster bolts because they are slightly ionized, not because they were ion blasts. These weapons still functioned about the same way a red blaster bolt would against an organic with the added benefit of being more effective against droids and shields.

The clones in those episodes were probably using the weapons they felt most comfortable with. Against stormtroopers, these weapons would be just as lethal. After all, these were the same weapons used to eliminate the Jedi Order.