The spelling of reconciliation is based on etymology, not on English pronunciation
Reconciliation is spelled with one L because the corresponding word in French and Latin is spelled with one L. The Latin and French spellings with one L are older than the modern English pronunciation. Between these languages and English, and also within English, the pronunciation of this word has changed more over time than the spelling.
The pronunciation of the vowel in the third syllable
The pronunciation in modern English has a "short i" sound in the third syllable. In the IPA, we usually write this vowel as /ɪ/. The vowel /ɪ/ is different from the vowel in the word see. The vowel in see is usually written in the IPA as /i/ or /iː/. The whole word reconciliation can be transcribed in the IPA as something like /ˌrɛkənˌsɪliˈeɪʃən/.
The related verb reconcile has a different vowel in the third syllable: the "long i" sound, usually written in the IPA as /aɪ/ (a diphthong, that is, a gliding vowel sound).
The alternation between the long vowel or diphthong /aɪ/ in the third syllable of reconcile and the short vowel /ɪ/ in the third syllable of reconciliation is pretty regular, and is consistent with the spelling of both words. The pronunciation of a vowel letter in English is sometimes related to whether the vowel is followed by a double consonant letter; but not always, and not in a straightforward manner ("short vowels" can be found before single consonant letters in this and many other words).
The pronunciation of the vowel in the fourth syllable
The pronunciation of vowel letters in English is usually not related at all to the presence of a double consonant letter before the vowel letter, so the fact that we don't pronounce the fourth syllable as "lie" isn't affected by the fact that we spell it "reconciliation" rather than "reconcilliation".