This little macro will check column A and determine on its own how far down the data belongs, then it will create a range of every "even" row in the range and delete them all at once.
Sub DeleteAlternating()
Dim RNG As Range, LR As Long
LR = Range("A" & Rows.Count).End(xlUp).Row
Set RNG = Range("A2")

For i = 4 To LR Step 2
    Set RNG = Union(RNG, Cells(i, "A"))
Next i

RNG.EntireRow.Delete xlShiftUp
End Sub