Wouldn't Israel view the newly minted Revolutionary Iranian government as a much bigger threat than Saddam's Iraq? What made the Israeli government decide to overtly support Iran and act as middleman for covert US support?
Israel was simply participating in what was then US policy -- See Iran Contra. As a regional ally it would be important for Israel to be a participant thus also making sure that it has some level of control over the covert relationship.
Also, the idea was to drag out the war as long as possible.
It is often claimed incorrectly that Israel's bombing of the Osirak reactor constituted help to Iran too, especially because Iran had "failed" to bomb the reactor itself but "only" damaged secondary buildings.
In fact Osirak was not part of a clandestine nuclear weapons program in Iraq but the bombing certainly encouraged that program
Furthermore Iran did not target the reactor core - which was not yet even completed - but targeted the secondary building where the high tech controls for the reactor were to be located.
More:
http://nationalinterest.org/article/the-osirak-fallacy-1093
http://fpif.org/is_the_success_of_israels_attack_on_osirak_a_myth/
http://www.pitt.edu/~gordonm/RW/ReiterPB.pdf
In general US support for Iran, whether direct or through Israel, was negligible compared to US support for Iraq, which continued from 1982 and expanded even after the Iran-Iraq war had ended. http://www.nytimes.com/1992/01/26/world/us-secretly-gave-aid-to-iraq-early-in-its-war-against-iran.html?pagewanted=all