If you use a FPGA and design a circuit, then it is possible. But not with an Arduino board.
You can try to set the bus speed to 200 kHz or 400 kHz with Wire.setClock().
If you need more speed, then you should use a sensor with SPI interface.
The Arduino Wire library was designed for slow 16 MHz microcontrollers. The Wire.endTransmission() and Wire.requestFrom() wait until everything is finished and the I2C bus is idle. That means the Arduino Zero has to wait a lot when using the Wire library. There are a few alternative I2C libraries, but I have not seen a good one yet.
Therefor the SPI bus is so much better when timing is important.
You are not using the old MPU-6050 I hope ? The MPU-9250 can do both SPI and I2C. It can do 1 MHz SPI, but for the actual sensor data it has a special high speed of 20 MHz SPI.