Sure, you can transplant now and bury it up to near the cotyledons (baby leaves).
Remember to fill the transplant pot right up to the top, it will slowly compact and shrink down over time. The more room for the roots allows your plant to grow its biggest. Don't worry about the stems strength, your plant "knows" what it is doing and as long as she receives good light strength, the stem will be up to the task. In 2-3 weeks you won't recognize your plant and the change in strength and structure will be remarkable.
In future, start your seedlings in pots, black plastic ones are great, that are about 4 inches across and 5 inches deep. This size pot will allow your seedlings to grow substantial root systems before they need to be transplanted. I constantly see people who want to grow giant plants, then start their seedlings in half filled paper coffee cups, stunting their plants from day one!
Remember too, a plants roots will be 2-3 times as long as the plant is tall, so shallow pots are really an inadequate start in life. For an idea of the size of a 3 week old seedlings root system, go to my diary "cannabis conundrums" and in week 7 there are pictures of the exposed root system. This may give you and anyone else that reads this, an idea as to why deep pots are so vital for a plants development, especially in the first days of its life and to be able to set it on a path of unbridled growth.
Hope this helps,............
Organoman.