Micro SD card power circuit failure
The residual +1V that you are seeing is being caused by bias on the other signal pins to the uSD card. Current passes from either high levels on the microcontroller I/O pins connected at the SDIO interface or via the 47K resistors that you have on these lines into the controller chip in the uSD card. From there it passes through the input protection network on these pins to the uSD card VDD pin where you see it appear at the 1V level. 

You can correct this situation by following the steps below:

1) Connect the supply line side of the pullup resistors to the switched VDD of the uSD card.

2) Whenever the microcontroller firmware goes to set the MICROSD_PWR_EN signal high to disable the card power set all output pins of the SDIO interface to a low level by outputting 0 bit values to their port register bits. Note that in some cases where the SDIO is enabled to an dedicated on-board peripheral on the microcontroller it may be necessary to set these output pins back to GPIO mode to allow the FW to gain control of the pins.

3) For any signals that are inputs to the microcontroller from the SDIO interface you need to arrange for these to go to a low level whenever the microcontroller sets the MICROSD_PWR_EN signal high. This can be done by one of two ways. You could change the 47K pullup resistor to a pulldown on these specific lines. Otherwise the input pins could be programmed back to GPIO mode and then set as outputs at a low level. This latter may be easier since then the I/O pins get handled the same as the output pins.

At the time the microcontroller goes to re-enable the uSD power by setting MICROSD_PWR_EN signal low the firmware would be written to re-configure all the SDIO interface pins back to their normal operating mode.