solution for mcu to configure ALTERA FPGA

Your solution looks fine.

There are a couple of things you need to consider;

1. If your microcontroller has DMA, then that can be used to reduce the CPU work-load.

2. Where is your configuration data going to come from?

A good option for configuration data storage is SPI or Quad SPI Flash. If your microcontroller has two SPI interfaces, this might be a good option. However, you will need to check that you can DMA from one interface to another. For example, Quad SPI is fast, so is often located on a "fast" internal bus, whereas SPI is low, so is often located behind a "slow" bridge.

I prefer to avoid these types "complications" by using a MAX II CPLD as the configuration controller. Eg., see

http://www.ovro.caltech.edu/~dwh/carma_board/fpga_configuration.pdf

Cheers,

Dave