Certainly there is. Embedded engineers replace and/or overwrite the bootloaders all the time. Here's an article on the subject but I'll outline the basics.
- Select a progamming device. There are numerous devices on the market, from very inexpensive to quite expensive, depending on what else they can do besides program a chip. You can even use another Arduino as a programmer, probably least expensive of all and readily available.
- Connect the programmer to the proper programming pins. For your purposes you'll want the ISP/ICSP headers (2x3 header(s)) on the board, or 2x3 connector to an non-Arduino programmer.
- Upload your code using the Arduino IDE, a utility such as AVRdude, or even Atmel Studio if you're very ambitious and want complete control.
It's not that hard if you use another Arduino as your programmer and 6 female-female jumper wires as outlined in the article.