Is there any rule for determining which is the more preferable pronunciation for a word with different pronunciation

"Association" is pronounced as either

/əˌsəʊsiˈeɪʃ(ə)n/

Or

/əˌsoʊʃiˈeɪʃən/

What I am focusing on in this example is the middle sound /ʃ/ -sh- which is made with ⟨ci⟩. Something came to my mind that there might be a rule in English which says that If a word has different pronunciations, the one which is made by different letters (here ⟨ci⟩) is preferred to other pronunciations which use a sound made by fewer letters (here /s/ made by ⟨c⟩ alone).

There are similar rules in other languages; for example in Arabic, if two words are synonyms the one with more letters is the preferred choice.

This is not determined by rule as there can't be really objective criteria to decide which pronunciation is absolutely preferable. The actual preference of a population as a whole can be determined through polling and the results communicated to users by means of notices in a pronunciation dictionary, and this is a feature of the "Longman Pronunciation Dictionary". It is a dictionary (for specialists) that treats thoroughly RP and General American. Here is a copy from that dictionary of two entries of the type you mention.

This dictionary (2000 edition) gives poll results for other types of pronunciations; before buying a recent edition of it you should make sure that this practice of providing poll results has been preserved (there is a 2008 edition and possibly a more recent one).

The answer by LPH brings up one of the problems here. "Associate" is often given two different pronunciations, depending on the use.

"Associate" as a verb commonly gets the long-A "-ate", while the noun/adjective form gets the "-et" pronunciation.

And other words are apt to be pronounced differently depending on the emphasis being placed on them or the sounds of the surrounding words.

As usual, this is English, so there are no "rules".