They bonded way before. They bonded on the night yejun ran away so he probably could be just fine since they were separated for five years before they meet again though the problem is the siyeon’s existence is already revealed to the alpha’s family and him being a hyper alpha is also now known.
Yejun was always tired and stuff for those 5 years and after being exposed to 'his alpha's' pheromones so much recently, wouldn't that affect him more this time if he were to leave again?
It depends on the rules the author puts up for the world. Not all Omegaverse stories share the same rules and laws. Some just tend to use the basic rules. This one it requires surgery to break the bond, and it comes with side effects, from the reactions they aren't good ones. It seems in this world they can still have sex with others that aren't their mate, with how we're led around with such hints.
Aren't the mc and the ml bonded? Are they? After having the siyeon? Can yejun leave even if he wants to without getting sick from being separated from his mate?