After watching the series over again, I came to conclusion that Smith probably could have assimilated the architect but couldn't.
Can Smith assimilate the Architect?
Architect is definitely well protected, probably via a strong firewall. Smith.exe, however, managed to infiltrate to the floor that supposedly can only be reached by the guidance of the keymaker. How he reached can be only speculated, however, assuming that he assimilatied other programs, probably created by the keymaker to guard the architect is a solid assumption. Had Smith.exe assimilated keymaker, he would also obtain his access privileges, so that he would exactly what is necessary to reach that level. This might be why agents prioritize the exile.
It is stated by the keymaker that only the one can access the architect. Here, we can speculate that since some code fragmentation of Neo is copied smith, he might access him and assimilate him.
Did Smith assimilate the Architect?
It is a recurring theme that when smith.exe assimilates a program, he also obtains his privileges. Therefore, assimilating a normal human offers him little advantage while assimilating another agents gives him much more power. That's why smith.exe used Oracle to fight Neo. Oracle, a powerful program that has many capabilities, including accessing to large variety of variables and using them to guess a future state of the matrix is indeed has the highest privileges and capabilities.
Had smith.exe assimilated the Architect, he would definitely used him. Architect, although lacks the intuitive capabilities of the Oracle, has actually designed the matrix and have control over every detail of it. For example, he has full access of Neo's emotions. It is unclear whether Oracle has this access.