Just as many other languages have, Japanese has gone through a number of both major and minor phonetic changes. English is certainly no exception, either. Why do English-speakers continue to spell words like "knight" and "daughter" as such when they no longer pronounce those words the way they are spelt?
Japanese has experienced the same problem of discrepancies between spellings and pronunciations as it is a rather old language. So, what have we done to amend them?
In 1946, our government announced a set of "rules" that basically said that words should now be spelt the way that represented their current pronunciations -- or at least as much as possible. The new rules are named 「現代仮名遣{げんだいかなづか}い」("Modern kana orthography") as opposed to 「歴史的仮名遣{れきしてきかなづか}ひ」("Historical kana orthography"). (Notice my cool use of 「ひ」 at the end of the latter term. That is an example of phonetic change, too.)
You can read (if you read Japanese) about the announcement of 現代仮名遣い in its entirety here on the official website for our Agency for Cultural Affair.:
http://www.bunka.go.jp/kokugo_nihongo/sisaku/joho/joho/kijun/naikaku/gendaikana/index.html
Moving on to the specific example of 「こおり」 vs. 「こうり」 for 「氷」.
The original Japanese word for "ice" was 「こほり」, or rather "ko + ho + ri" when Japanese was only a spoken language. It was a 3-syllable word containing 3 distinct consonants. It was not an almost-2-syllable word with an elongated first syllable as it is today.
Now, let us consider the word 「高利{こうり}」("high interest rate"). It never was 「こほり」 to begin with. Thus, it is still spelt 「こうり」 in kana currently. As you know, it is pronounced like 「こーり」.
(It might help to remember that there is no 「おお」 in Sino-loanwords written in kana. There is only 「おう」 as there never occurred a ほ-to-お sound change in how Sino-loanwords were pronounced in Japanese.)
Therefore, as a sort of reminder of the historical origins of the words, our 現代仮名遣い rules say that 「氷」 should be spelt 「こおり」 in kana and 「高利」 as 「こうり」 even though both words are pronounced like 「こーり」 in present-day Japanese.
Incidentally, 「氷{こおり}」 is specifically mentioned in the above-mentioned new rules. Read #6 here:
http://www.bunka.go.jp/kokugo_nihongo/sisaku/joho/joho/kijun/naikaku/gendaikana/honbun_dai2.html
Mind you, 現代仮名遣い is not a perfect invention. For instance, as you know, particles 「は」,「へ」 and 「を」 are still written as such even though they have long been pronounced 「わ」,「え」 and 「お」, respectively. How words "look" is still important, our government must have thought. At least in the case of 「こおり」, even the first-graders know how to read and write it in kanji (「氷」); therefore, we still managed to maintain the appearance of the word.
Fortunately or unfortunately, we did not have the English problem of possibly having to re-spell "knight", "daughter", etc. so that the words are spelt according to their current pronunciation while still keeping the good, physical appeal of the words.