If you don't want to use the kitprog programmer on CY8CKIT-059 kit, there is a provision for removing the daughter board.but, then you may need MiniProg3 to program the PSoC5LP on kit.
I think you are mentioning about diode D1 to be removed on CY8CKIT-059 kit.We have not checked doing so experimentally.But, diode D1 provides connection between VBUS and VTARG signals.
Without VTARG connection programmer kitprog will not br able to program the target PSoC5LP chip.
The schematic of CY8CKIT-059 at this link-
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I have separated the two pieces, and added a header to the CY5888 side, and a cable with five pins to the programmer side. This allows me to connect the module to my project (which powers it) or to the programmer to reprogram it. I did not remove the diode.