Unfortunately, this is not possible. An EEPROM write uses the SSC instruction to access the Flash write functions. When SSC instruction is executed, the global interrupts automatically get disabled. When you write an EEPROM block, it takes around 20ms to write to the Flash block. Will this 20mS latency be a problem in your application?
Would you please elaborate the statement that "the Interrupts are disturbed". Also, if you are using I2CHW module and I2CHW_fSendStart() and I2CHW_SendStop() API, then these APIs disable the I2C interrupt, so it needs to be enabled again and pending interrupts of I2C has to be cleared.
If you don't want this to happen then you can wait for some time to complete the write or read transaction. This can be done by a normal for loop.
Also, there is an example project on CY website which might be helpful to you. Here is the link for that project: http://www.cypress.com/?rID=34661.