Linguistics classes seem to be mostly concerned with analyzing language in its spoken form. Written language is seen as almost "parasitic" to spoken language. A language's orthography generally gives an unreliable reflection of its structure. As such, I've been told that you only need to examine language in its spoken form to understand its morphology. However, I feel that this is a rather myopic approach to morphological analysis. For example, consider the relationship between the words 'sign' and 'signify'. Note that 'sign' has a silent 'g', where 'signify' does not. Casually browsing the online etymology dictionary, you can observe that the Latin word 'signum' evolved the old french word 'signe', which evolved into 'sign', which in turn evolved into 'signify'. The orthography, though unstandardized at the time, may explain how /g/ remained recessive in 'sign' and was transferred to 'signified'. I understand that pronunciation was very different in the early 13c, and that this probably is not a very good example. (I know nothing about historical linguistics.) There are probably other processes at work for my specific example. But I hope you can understand the concept which I am trying to convey. Why don't we consider a language's orthography when doing morphological analysis?
It is not correct to say “that the Latin word 'signum' evolved into 'sign', which in turn evolved into 'signify'”. The English words “sign” and “signify” are both borrowed from Old French, which had them from Latin. English does not allow the cluster /gn/ in word-final position; that is why the /g/ is lost in “sign” but retained in “signify”. It is about phonology, not orthography.
Common knowledge of writing in a society can and does have an effect on the language structure, and it's been noted:
There's this Israeli linguist (I've forgotten his name) who says so-called Modern Hebrew isn't really a Semitic language... he argues in one of his books how Chinese writing has had a profound effect in the language, by altering the way new words are created and how borrowings are adapted.
I vaguely remember Saussure mentioning in a sentence in one of his books "I've been told people in Paris now pronounce the 't' in 'sept' ". I found that really odd, for I had been taught uttering "set" was THE correct way to pronounce 7 in French. So clearly Parisians of his time were adopting an artificial pronunciation based on spelling, which then was declared the standard.