Long story short, you made winning OW battle into a requirement to conquer a territory. Small guilds will simple have no chance to conquer anything at all. Big guilds out of alliance - maybe will be able to hold some territories nobody really need. Everything else - belongs to the mega alliances, and eventually one mega alliance which will emerge as more successful at attracting numbers.
PS. Proposed changes is a copy of Dominion mechanics from EVE. It taken like 5 years to get rid of it in EVE and damage was already done, EVE nullsec is basically controlled by a single entity. At least EVE do have huge battles as one of desired scenarios, and Dominion did provide the community with AO Gold. Its just resulting political map is less than great. In Albion i cannot imagine anyone wanting huge battles, nevermind servers unable to process them, interface and an overhead view will make 200 vs 200 or more into pure chaos.
Have you seen the alliances that currently own 60% or more of the map?
Small guilds will always struggle to do the same things bigger guilds do. Being in a small guild takes more discipline, organization, and skill. When you are in a zerg guild you will have less ability to fight when you don't have your zerg because you will not have the practice you need and a small guild who is experienced will handily destroy you.
Trying to make it so small guilds compete on the same level as zerg guilds is an impossible feat. Mitigating the rewards of large alliances that take over all of the map is what needs to be done with game mechanics that specifically target it. Make upkeep on territories go through the roof the more you have of the same type.