I don't think there is way to change the Clock Speed of KitProg. If you have a MiniProg3, use it for programming and debugging the target PSoC 5LP directly.
BTW, have you tried powering the kit with external supply so that KitProg SWD lines do not interfere with the target PSoC 5LP while running your application?
Thanks for your answer.
In this case I will use the MiniProg3 programmer and insert the isolator either between MiniProg3 – target or USB – MiniProg 3.
To power the KitProg with an external supply is not useful in my application. I need some galvanic insulation to protect my PC.