Will Trump Run as an Independent now?

I don't think that is the problem. The problem looks different than that at least for now.

The problem appears to be that 20 plus Senators who are Republicans and many Congresspersons who are Republicans may not be re-elected or elected for the first time which could result in a Democratic Controlled Congress AND a Democratic President (Likely Hillary).

At least one Republican Senator has come out publicly to declare he will not Support Trump(no matter what already).

Though Senator Sessions has endorsed Trump and Christie has endorsed Trump, there are no other Republicans that I presently know of who have endorsed Trump which is unusual this late in an election year for a front runner.

So, though it is less likely that Trump will run as an independent I wouldn't completely rule it out. But, if he runs as an independent just expect Hillary to win in a 3 way race.

So, at present it looks like Hillary is the next president almost no matter what the way things presently stand.

Any way you look at this it likely will tear the Republican Party apart this year before, after and during the Republican Convention.