Well of course packages including Mirages should have had some kind of EW/Jamming/Wild Weasel provided the enemy's anti-air capabilities were deemed potent enough. Warplane packages aren't simply a large number of a singular type but a multi-faceted construct allowing various elements of that construct to work at their optimal roles. And as much as the IAF initially held up their nose at the Mirage III, look at their combat history - they did extremely well with the platform, coupled with early, almost primitive but definitely effective EW systems and significant use of drone decoys to open up missile locations for destruction or avoidance.
I don't think comparing the Mirage III's systems to that of the F-15 is very helpful. Those planes are separated by cost, modernity, requirements, along other things. The Eagle is probably my favourite of all the teen-series but it was absolutely not on the table at the time Mirages were being purchased. Although you might be interested to know that the Kfir local Israeli Mirage variant makes use of the same J79 engine you mentioned. But that was a number of years afterwards.
To stay on the aircraft theme, Israel did indeed procure a number of F-4E Phantoms (along with the recon variant if my memory is correct). A truly beautiful aircraft and probably one of the first true multi-role jets (drops LGBs on target, kills a hostile on egress with a Sidewinder or Sparrow, and in the E variant discussed, retention of an internal gun for more accurate ground support and another tool in the box for air-to-air, especially considering the state of missiles around Vietnam. Podded guns were of course available for earlier designs but they suffered significant accuracy problems if they weren't boresighted properly.
I agree with you on the R-530, that's why I consider 2-3 drop tanks (not sure if the centreline hardpoint was plumbed but seems logical that it would be), a pair of Sidewinders, and a pair of 30mm cannon to be the logical loadout. You might just be able to squeeze 4 Sidewinders depending on the weight capacity of the wing hardpoints. I wouldn't even bother with semi-active missiles of this period besides the occasional Sparrow success story. I think a small, fast jet with rear aspect seeking missiles and guns to back it up could have changed the picture of how dogfighting was done (though obviously the Phantom became the most important platform in terms of air warfare thinking and development).
Anyway, back to the Navy, I'm just a sucker for historical combat aircraft of any era.