From the documentation, setting INITRQ effects:
"The following registers enter their hard reset state and restore their default values: CANCTL0, CANRFLG, CANRIER, CANTFLG, CANTIER, CANTARQ, CANTAAK, CANTBSEL."
Do you reenable interrupts after changing bitrate?
Another quote regarding recommendation to enter sleep mode before setting INITRQ:
"In order to protect from accidentally violating the CAN protocol the TXCAN pin is immediately forced to a recessive state when the Initialization Mode is requested by the CPU. Thus the recommended procedure is to bring the MSCAN into Sleep Mode (SLPRQ=1 and SLPAK=1) before."
As I understand it, sleep is recommended to prevent sending incomplete message. Though this can be controlled by software, "just don't send anything if you are going to init mode", but you can't control easily acknowledgement of messages sent by other nodes. Switching from dominant to recessive in the middle of ack bit is not something very nice. But I don't think you can't enter init mode without intermediate sleep mode.