I rode a 49 cm Bianchi with 700's for 8 years in absolute pain and torture. I am super petite, 5'1 (110 pounds) but I have a very short torso and almost a 31 inch inseam. After many injuries and much suffering, I bought a 46 cm Guru (road not triathlon) with 650's. I love my new bike. I like the feeling of being able to control it. I like a bike with fast response. It's also immensely lighter. I like how the bike feels in corners, climbs, and descending. I feel more in control. It feels 'lower' to me than my other bike and I like this.

It's my second full season with my newer bike. It did take time to adapt to it. So, I say stick with the new bike for a while, especially if your only consideration is being 'higher.' If the new bike fits and is comfortable, I'm sure you'll be feeling better soon Let us know how it goes