This isn't really about cost, indeed, it may not be a cost-saver, but intending no offense I'm pretty sure I'd want a second opinion before I'd consent to sedating a three-year old for dental work.
Also, your post doesn't address this at all and it may be it's something you already have all the information you need about and are totally on top of, but if you're not 100% confident that's true, in your shoes, I'd want to be sure I had good information about and was doing a good job cleaning my child's teeth (indeed, appropriately managing dental hygiene is 100% something I always talk both my my own hygienist and with my 6-year old son's about; it seems like I'm always learning some way to do something better). It's not that 2 cavities sound like the end of the world, but it does sound like it's probably toward the high end of what might reasonably be expected. This too could be an argument for seeking out another dentist -- I've found real variation in how good dentists and the hygienists who work with them are about communicating effectively about this.