Deuterium is not like gasoline or other fosil fuels which are heated to produce the needed gasses for propulsion. Deuterium is combined with antimatter to create a annihilation reaction which creates the power for the warp core.
When one examines the challenges in manufacturing antihydrogen, it becomes clear that there is a need for "cold" antihydrogen, which can be kept in a magnetic trap in order to be utilized. Antihydrogen is synthesized by bombarding xenon clusters with antiprotons, to create electron-positron pairs.
As the matter reactant in a warp reactor, the deuterium obviously needs to also be of a low energy level, so it is "cold". This makes sense when you are trying to dilithium-regulate what must be a massively exothermic reaction.
A warp-core containment breach must occur when the magnetic trap, or "magnetic bottle", ruptures, and there is runaway deuterium-antihydrogen annihilation as a result, destroying ships aboard which such breaches occur ProfessorTrek 02:43, August 2, 2011 (UTC)
The temperature doesn't really matter when it comes to energy release. Einstein's equation explains that as long as there are equal amounts of matter and antimatter then when both substances come into contact all the matter and antimatter is destroyed releasing energy. According to memory alpha it isn't a deuterium/antihydrogen reaction it is a deuterium/antideuterium reaction which actually mean hydrogen/antihydrogen since deuterium is just an isotope of hydrogen so antideuterium would be an isotope of antihydrogen. Current technology only allows us to create infinitesimally small amounts of antimatter and the lowest temp we have reached is still a few thousand kelvin. For something like Star Trek there will have to be a complete revolution in techniques for creating antimatter molecules as it stands it would take 100 billion years to create a single gram of antimatter.