How to configure STM32 with two different clock speeds
When it comes to programming the STM32, the RM0008 Reference Manual should be your constant companion.

Section 7.2.3 PLL:
If the USB interface is used in the application, the PLL must be
programmed to output 48 or 72 MHz. This is needed to provide a 48 MHz
USBCLK.

So it's not only possible, it's one of only two possible frequencies you can choose when utilizing the USB.
You should be able to set the system clock to 72 MHz using the defines and functions in the STM supplies libraries. But your RCC_CFGR looks okay. You've got HSE selected as your PLLSRC. And you're setting the PLLMUL to x9. So as long as your HSE is supplied by an 8 MHz oscillator (which it looks like it is), you'll get 72 MHz to the SYSCLK. And you have USBPRE set to 0 so that will divide the PLL by 1.5 to get your 48 MHz.
Looking at the clock tree on page 90, that looks like all that is required.

As for accessing flash, you need to make sure you have two wait states. That is done by writing 010 to the FLASH_ACR register. See page 60 for more detail on that register.