Yes, the remote side I2C bus can run at a different speed than the local side.
In a GMSL system, the controller is connected to the local device, while the coax/STP cable connects to the remote device. The remote side does not care about the I2C data rate of the local side. The I2C commands that the master controller sends are received by the local side, then sent across the link using the GMSL protocol. The remote side decodes the GMSL protocol, then sends I2C commands to peripherals based on the settings in register 0x0D in the MAX96705\6. In this register, you can set up the bit rate, setup/hold times, and timeout settings. See below for an example.
In a camera application, the serializer is typically connected to an image sensor on the remote side, and the deserializer is connected to a processor on the local side. The processor sends I2C commands to the deserializer, and the deserializer forwards the I2C commands across the GMSL link to the serializer. The serializer acts as an I2C master to the image sensor. So, if the processor is running the I2C bus at 400kHz, but the image sensor requires a 100kHz I2C clock, set the I2C_MST_BT bits to send data at 100kHz.