"::""Analysis suggests that it was an air to air missile"" is enough for it to be confirmed. A MiG-25 was the only aircraft in the area and there were no SAMs there too.
Are the words of a Navy commander who flew that night and saw the MiG before the shoot down and a naval intelligence officer who investigated this not considered primary or credible by you? The article was only opinionated about why was this air-to-air loss not admitted in the first place, not about whether it happened. 
Here is what the naval intelligence captain says:

""We were pretty sure at the beginning. Then, by the end of the war, we were pretty much able to prove that [the attack] was the only logical explanation - other than his aircraft disintegrating.""

Iraqi Air Force's archives? I read that much of them are destroyed. Anyway, the Iraqis did not even claim the kill probably because the pilot was not sure that he downed the F-18 or there was not enough confirmation for it before the US admitted it.   

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