It all depends. Let's take a look at your situation. There're 2 possible options (depending on whether your actions would be considered fleeing). However, the following is just my point of view on that matter.
1) Let's assume that your docking counts as fleeing. Then the interaction is over, and the merc died to NPC, thus he didn't die in PvP.
2) Now let's assume your docking doesn't count as fleeing. In this case you simply finished the interaction by docking (taking another ship and getting back should count as new interaction, if you ask me). Thus, the merc didn't die in PvP either, since it never started.
In case one, you'd have to leave the system, while the merc wouldn't. In case two nobody would have to leave the system.
However, the question whether your actions are considered fleeing or not still stands.
