There is no way to know WHY he removed it. All that can be done is look at what he did. He removed the clause.
He didn’t want it there.
And that is significant.
"No person shall be eligible to the office of President of the United States unless he be now a citizen of one of the States or hereafter be born a citizen of the United States"
James Madison himself said: "It is an established maxim that birth is a criterion of allegiance. Birth however derives its force sometimes from place and sometimes from parentage, but in general place is the most certain criterion; it is what applies in the United States; it will therefore be unnecessary to investigate any other."
For further reading on the founders views of a Natural Born citizen with extensive quotes, with the clear conclusion Ted Cruz is a natural born citizen: http://www.redstate.com/2012/05/21/on-this-natural-born-citizen-issue-part-i-from-alexander-hamilton-to-lynch-v-clarke/