Therefore, can I just disable the Auto-Negotiation function?
You could but you shouldn't. You should leave Auto Negotiation enabled at all times. There are very few scenarios where it makes sense to disable it.
With Ethernet over twisted pair, disabling AN is a common mistake that sooner or later lands on your feet unless properly documented. It's mandatory for 1000BASE-T and faster anyway.
By IEEE 802.3, Auto Negotiation for 10/100 Mbit/s and fiber is still optional, so hardware often allows disabling it.
In practice, it's not a bright idea to do so unless you've got ancient, non-compliant hardware and know exactly what you're doing - manual configuration always has to match on both sides of the link (speed/duplex/pause mode). Mismatching the speed won't bring up the link, but mismatching duplex modes enables the link but makes it perform extremely poorly.