That whenever any Form of Government becomes destructive of these ends, it is the Right of the People to alter or to abolish it, and to institute new Government, laying its foundation on such principles and organizing its powers in such form, as to them shall seem most likely to effect their Safety and Happiness.
The arguments in the Declaration of Independence go much further that simply stating the colonists have decided to self-govern in accordance with their natural right to self-determination. The stated justification was not simply an explanation to tell the world why they thought independence was worth fighting for, or to attract more people to the cause. The opening lines present a moral and philosophical justification for revolution, which a modern understanding of democracy considers irrelevant. Self-determination does not require compelling reasons, or any justification at all, beyond stating that independence would be in the best interest of the people.
Jefferson and the founding fathers seem to have accepted an understanding of civil society which did not allow secession except with extreme justification. Self determination would not have been a sufficient reason to break their ties with England. They were clearly a distinct political entity which was sufficiently mature to govern themselves, and to a large degree they were managing their own affairs before the Revolutionary War simply due to geographical considerations. Still Jefferson found it necessary to explain the circumstances which compelled them to rebel against the Crown.
A purely individualistic approach sees government as external to the people, managing their affairs much as the post office manages their mail. The government does not reflect any inherent relationship between people.
But individualism and democracy are not synonymous. Democracy does not depend on an individualistic philosophy.
People are held together by community and social ties which precede their common governance. When they do set up a formal government they may well choose democracy in acknowledging the value of each individual, but it is not the common government which unites them. It is the common social existence which unites them into one body which forms a government to manage its own affairs.
The individual members of the society are all committed to each other to promote the general good. A member of society who does not care about his effect on society is a parasite, as he is part of the social body but has no interest in its wellbeing. A large demographic is also still an integral part of the society. If they challenge the government they are turning against their own society which they are part of and morally committed to. Unless they can demonstrate serious grievances they are morally committed to their native society. The rebellion against the Crown does not need to be justified, but the split with the host society does need to be justified.
The main difference between the founding fathers who felt a need to justify their move to independence and the modern sensibility which sees self determination as a given is their view of society. They saw society as an organic whole, and expected a moral justification for a decision to split the society. The modern view just sees individuals with no connection to each other except for geographical proximity and their need to form a government in common.