There are plenty of ways to worm out of such drawbacks. Note that my original post stated you get points "per action" not "per battle", so one way to avoid the problems you mentioned would be to have the class change occur automatically during battle whenever you've met the conditions.

Each time you use a physical attack, you'll notice it getting stronger until your class finally changes to Warrior, Knight, etc. Each time you use White Magic, you'll notice it getting more potent until your class changes to Paladin then to Sword Saint (assuming you're still using physical attacks), and to White Mage, then White Wizard (if no longer using physical attacks). If, from Fighter-Warrior-Knight, you use Black Magic enough, you'll go from Red Mage to Red Wizard, or to Black Mage and then Black Wizard. On the other hand, spamming attack will eventually promote you to Berserker and put you in berserk state until the battle ends (the next battle would revert you to the class prior to Berserker). As a counterpoint to this, spamming black magic would promote you to a Fury (a magic Berserker inspired by Lulu's Overdrive).

To avoid Job Classes shifting right when you've got them, the point counters will reset upon reaching a class, and a priority system measuring your overall use of skills (percentage rather than grand total) will prevent shifting to a job class you weren't even shooting for. As a helper for those wanting to boost their summon attacks, you can use more affordable black magic and it will also increase the power of your summons for when you're ready to use them. However, using Summons doesn't add points to Black Magic and there is no berserker-style risk to spamming summons.

You always have access to any command and every magic spell as your job class only dictates how potent those abilities are. As you upgrade from Mage to Wizard, your spells will automatically shift to Ra and Ga spells, the MP cost shifting with the change. But your Class change would adjust your MP's percentage not just the maximum so really the only moment a class change would affect your ability to cast is if you were already next to zero.

Balancing points would not only lead to the creation of Red Mages and Paladins but to other job combinations like Samurai Knights, Assassin (Ninja + Ranger), Dragoon (Ninja + Gladiator), etc.

Being able to shift to any class at any time, you can equip any and all items you find, however, Heavy Armor will slow down classes not meant for it and certain weapons will be all but useless unless you're the proper class (i.e. Bows and Arrows, Bells, Books, etc.)

That's all I can think of at the moment.