I would travel with an inflatable booster seat for the two year old and just use a taxi from the queue with the regular seat belts. If the five year old is very small, you could use the travel booster for them as well.
The only safety concern for the metro is stairs and little kids and stuff. Pickpockets will be at every tourist site you visit so the only solution to securing valuables is to not be a walking buffet. No valuables in pockets -- for transit situations like this I use a money belt under my clothes for money, cards and passports and my phone is in a lanyard carrier under my jacket. Don't put small valuables in backpacks and be sure you always have your hand on things like a computer bag.
but I'd get a cab, use the portable booster seats for the kid or kids, and stow my stuff and then head out and use the metro for getting around Paris once the valuables and bulky stuff is stowed. The 2 year old is free; tickets for the 5 year old are half price if purchased on a Navigo Easy card. If you are there a week or so. Mon-Sun, then a Navigo Decouverte pass for the three oldest of you will give you unlimited bus, metro and RER in the Ile de france.