Knowing that Oberyn's prime motive was to avenge his sister, he would make sure that The Mountain would suffer even if Oberyn himself lost. Given his strong desire for vengeance, he may not have even volunteered as Tyrion's champion if the Crown's champion were not Gregor Clegane. Sure, he felt a bit sorry for Tyrion when he recounted his experience of meeting an infant Tyrion, but if you weighed Oberyn's empathy for Tyrion against his desire for vengeance, you'd find that revenge greatly outweighs empathy.
Unfortunately, in the end, Oberyn was too wrapped up in trying to exact his revenge that he lowered his guard just long enough for The Mountain to kill him. If Oberyn weren't clouded by his desire for revenge (hence a normal 1v1 combat), Oberyn could have bested The Mountain. Look at his style of fighting: he's light on his feet, agile, and knows The Mountain's weaknesses (Gregor Clegane suffers from bad migraines and is almost always on Milk of the Poppy, and Oberyn's constant shouting and taunting disorient him). If Oberyn were not so emotional during the fight, he would have kept the upper hand easily. For a similar battle, remember Bronn vs. Ser Vardis: Bronn was light while Vardis was heavily armored. Bronn knew he couldn't win head-on, so he tired out Ser Vardis until he had the upper hand. Oberyn was fighting the same sort of battle, except his emotions clouded his better judgment.
Now, whether the poison actually finished off The Mountain or Qyburn's mad science has created a Fraken-Gregor, we'll have to wait and see.