PCI: don't corrupt enable_cnt when doing manual resource alignment

This patch fixes breakage of of enable_cnt in quirk_resource_alignment.

Currently, quirk_resource_alignment calls pci_disable_device.
pci_disable_device decrements enable_cnt, so that enable_cnt becomes -1.

The patch disables memory decoding, writing command register directly.
So enable_cnt is not broken.

Signed-off-by: Yuji Shimada <shimada-yxb@necst.nec.co.jp>
Signed-off-by: Jesse Barnes <jbarnes@virtuousgeek.org>