1. Should I only run a node if I have an educated opinion about protocol development?
No. Anyone and everyone should be running nodes.
i.e. if there is a proposed change and I don't know precisely if the proposal is a good thing for the network, would I be inhibiting the network?
Given that most protocol changes are soft forks, you would not be inhibiting the network. If a hard fork were proposed, you should continue running your node until you have studied the hard fork proposal enough to understand what it is doing and its ramifications before you upgrade to software that supports such a hard fork. Having node operators be critical about changes that are happening is a good thing and helps with the Bitcoin network's robustness.
2. Should I consider running node software that ISN'T core, so as to "decentralise" the network in that regard?
You should consider it, but there are very few alternatives to Bitcoin Core.
However different implementations of the consensus rules is not necessarily a good thing. All implementations must be bug-for-bug compatible with each other, and that is unlikely to happen given different implementations and languages. It is likely better for the network for all nodes to be simultaneously taken down (which is what would happen if everyone ran the same software) rather than it partitioned and the blockchain accidentally forked (which could happen with different implementations).
3. What are those alternatives called?
I only know of two other full node implementations: btcd and bcoin.
- What procedure do you recommend to scan my computer for viruses/malware? Is a reinstall of windows sufficient? Is it more secure to run linux as a second operating system for this purpose?
Running a anti-malware scanning software should be sufficient. If you are feeling particularly paranoid, then reinstall your operating system. Note that Windows 10 itself relays a lot of data back to Microsoft, so you should disable those settings.
- (although I don't see this scenario occurring for a little while) Is it possible to use the funds in that wallet away from home? (i.e. using a phone app or something?)
You could set up some sort of remote access (e.g. SSH, Remote Desktop, Teamviewer) and access your computer from your phone to spend your coins.
- As I have been advised to use a virtual machine: If my local computer is affected by some type of virus, wouldn't the virtual machine also be vulnerable?
Generally, no. A virus needs access to your wallet files. With a virtual machine, your wallet files are stored in a virtual machine disk file, which makes it harder for a virus to access the file and steal it. While they could do that, I find it unlikely to happen.