Barring some unforeseen changes to the situation between Adam Rubin and Omar Minaya, here is my take on the matter.
One of the first things I learned in my journalism classes was to never make yourself part of the story. Yesterday, Rubin had no control over it. Minaya pulled his name out and tried to drag it through the mud. Rubin had to respond with a press conference of his own to clear up the insanity.
Most people are taking sides on it, but I stand firmly in the middle. Both parties were wrong.
Rubin, though interested in a job in baseball, should not continually (or even once) “lobby” for a position or even inquire with officials of the team he is covering. Maybe another team, in another league. Maybe. Otherwise, this just seems like a huge conflict of interest if anyone does lend a hand his way while he may be covering the team.
Edit: Rubin said something to the effect of talking to people about a career in baseball. That might not be lobbying (hence the " ") but it is something to note. Minaya could be fabricating this “continuing lobbied” story, or it could be true. Even if Rubin once asked Jeff Wilpon or anyone else with the Mets about a job with the team, I think he crossed some line.
Minaya, though somewhat just in his suspicions, should not have slapped this on Rubin during the press conference that was being broadcast on TV. If he took Rubin aside and spoke to him, that would have been fine.
Rubin should, and has, stood by his reporting. His articles brought to light a very serious matter within the Mets and they conducted their own investigation because of it. The team must have found something to back up Rubin’s story, otherwise Tony Bernanzard would still be employed.
Sure, it could have just come from fan pressure that they let Bernazard go, but I don’t see that being the reason. They must have found a red flag (or a few) in order to go through with canning a dear friend of Minaya and Jeff Wilpon.
Rubin did some great reporting to break the story and defended himself against the acqusations that he was gunning for Bernazard’s job. But Rubin did trip up in his press conference and appearance on TV afterwards.
He said, on many occasions, that he doesn’t know how he’s going to cover the Mets anymore after this.
That’s a big no-no to me. As a journalist, you have to stay emotionally separate from your story or beat. You cannot spill emotion into a news article. That’s for a columnist or fluff article. You must report the facts whether you like them or not, because what you think as a reporter doesn’t really matter.
If you do see a discrepancy or some fault, you can further investigate, but your personal feelings should never, ever creep into your articles.
If he believes that, as a reporter, he won’t be able to continue to find the true facts on the team, that may be one thing. I don’t believe that was what he was alluding to, though.
So both Minaya and Rubin were at fault. Minaya should not lose his job over this. Either should Rubin (though as he said, he doesn’t know how he’s going to cover the team anymore). Both probably said things they would take back in a second.
This story seems like it has some legs and will keep chugging along for a few days, at the least. As a journalist, it is fascinating and horrifying to watch.
It might be more exciting than the Mets season.
Mandeep and Shavarish, from NY NY Sports Sports, took their first trip to Citi Field last night.
Oliver Perez pitched an Oliver Perez-like game, allowing three earned runs in five innings. He needed 103 pitches to get through the five frames. He walked four and struck out five. 
“He's been on fire. He's doing everything. His game is impeccable at this point.”