PvP can be fun. When two or more individuals go and test out their creations in a slug fest to see who will come out on top can be both very entertaining and fun. However, getting to a place on a server where one can do that is not always fun and depending on the server population and behavior, can be quite toxic.
Ideally, one will join a server and find a place to call their own, then set up shop, make a faction, and then start gathering resources for ship creation. At some point they if will finish up their ship and go out to test it. This test could look like a sanctioned duel, where the player asks another player to combat for the purposes of testing out the ship. The test could also look like the player attacking an AI pirate station to see what they can do, or lastly they could go and attack another player to see how they fair.
The issue is not solely about losing valuable resources, but about not being able to use those resources to create something to play with. If a new player is mining and working on getting to a place where they can stand on their own, but is attacked by the Pirates and killed they chalk that up to bad luck, or just bad timing, and the same could go for a single attack from another player. However, if the new player comes under attack from the same player or even the same faction more than once it is likely that they will either, try to join the attacking faction, join a faction that can protect them, or if that fails complete leave the game.
I agree that galactic conquest by a single faction/player is not going to allow for a reasonable player environment in a MMO-Sandbox. Neither is allowing for a single player to hold a monopoly on resources in the MMO-sandbox. Having multiple factions that are both there to help out players, but also drive PvP is another way for this to go. I nearly every successful MMORPG, the players at creation choose a faction to fight for, and from there gain a noted enemy, and a noted Allie from the start, with defined boarders of where safe is and where safe is not. Having AI a driven faction that could come to the aid of its members (While exploitable for resources), could be one solution to how to make PvP more PvE friendly, where home base protection would not change, but being in a controlled sector would have the benefit of AI spawned protectors if needed, and non controlled sectors have no protection.