Dear Ghoti,
.NET is not a part of Windows persay, in that you can install it without upgrading your operating system. .NET is a development environment which did not come with Windows XP so you need "runtime" libraries so that the program can execute.
So to answer your questions:
1) No you will not find yourself in any upgrade, you can install the libraries without any lasting affect to your operating system. Similarly you will be able to uninstall the .NET software with no affect to your machine.
2) If the software requires these libraries then there is no alternative but to install them.