msm: pcie: adjust pipe clock management

When PCIe PHY is powered down and powered on, the pipe clock from
PHY will result in GCC being stuck "on" and "off", respectively.
This outputs the clock warning for GCC clock, although the
functionality of clocks is fine. Adjust the pipe clock management
here to avoid this kind of clock warning.

Change-Id: I89958acc4a8b202e1d3950ac98f8690463e562f1
CRs-fixed: 580991
Signed-off-by: Yan He <yanhe@codeaurora.org>