"Sovereignty" isn't the only noun ending in "-ty" instead of "-ity". We also have
- royalty, loyalty, cruelty, fealty, frailty, penalty, admiralty
- liberty, puberty, property, poverty
- honesty, majesty
Some of these are from Latin words that didn't have "i" in this context: e.g. liberty = L. libertas, majesty = L. majestas (maiestas), puberty = L. pubertas.
Others are from French, where the suffix -té is fairly often not preceded by "i" (Latin vowels are often weakened or lost in French): e.g. cruelty, according to the Oxford English Dictionary (OED) from
Old French crualté (later cruauté), according to Hatzfeld < popular Latin type *crūdālitāt-em, for crūdēlitāt-em (see crudelity n.)
Some of these are related to words ending in -ity: although "crudelity" is extremely uncommon, there are words like "regality" (from the same etymological source as royalty) and "fragility" (from the same etymological source as frailty). Property is related to propriety: the suffix has the form -ety here because of the preceding i.
You can see some more information about the Latin suffix -itas/-etas/-tas and the distribution of its variants on the following page: "§46. The Latin suffix -ITAS (> E -ity); variant -ETAS (> E -ety)" (Smith, Peter. (2016). Greek and Latin Roots: for Science and the Social Sciences, Part I – Latin).
The etymology of sovereign
As mentioned in user159691's answer, sovereignty comes from French. The OED says
< Anglo-Norman sovereyneté, soverentee, = Old French souveraineté (modern French souvraineté)
The word sovereign is supposed to be from
popular Latin *superānus (OED)
As you can see, there isn't a "gn" in the Latin source (it is thought to come from super + the Latin suffix -ānus; compare christian and christianity from Latin chrīstiānus, chrīstiānitās).
The digraph "gn" was probably introduced into the English spelling of "sovereign" by mere analogy with other words spelled with word-final "gn" (according to Etymonline, proabably association with the word "reign" in particular).
The OED does list a few examples of "sovereignity" with "-ity", but says this word is obsolete. The earliest example it lists, from "c1560", uses the spelling "souerenitie" without "gn". The OED also mentions the related word sovranità in Italian.
"Gn" does show up before "ity" in words where "gn" comes from Latin, like benignity and malignity (Italian benignità and malignità). In English, the letter "g" corresponds to a consonant [g] that is pronounced in these nouns, although there is no [g] in the pronunciation of the adjectives benign and malign.