I agree with the idea that Santander is better to keep Gran Colomobia united than Bolívar. However, I'm not sure if this would be better for the grancolombians. Considering how violence got encocrched in the political life of the constituent countries of Gran Colombia in OTL after the independence wars and the internal conflicts, what I can see is something like Mexico's OTL infighting amongst regional elites/ regional elites against central elites etc on steroids. Also, Nueva Granada was relatively poorer and less developed than New Spain, so the start from a more difficult position, and if their independence war goes like in OTL also with more destruction (both material and in the social tissue) than Mexico. Finally, Bolívar, with all his flaws, his lack of vision regarding the structural difficulties to his project and the way he apparently lost his mind a bit in older age, at least had an actual will to make better lifes for his people. Santander, on the other hand, was your tipical criollo who doesn't gave a shit about the means to reach his goals.
Also, we can try some giant butterflies, but with a wider perspective.
One of them should have a POD in colonial times, with a more coherent, integrated vicerroyaltiesthat are something that an administrative line enclosing local and regional entities without much actual connection amongst them (I'm talking about economics and infrastructures) In this case, however, everything should be so different in the early 19th century that probably is going too far.
Another option, more feasible, would has its POD not in Gran Colombia, but in México. If the Treaty of Córdoba goes ahead (Juan de O'Donojú survives, the spanish Cortes are more sensible, Ferdinand VII has an ictus and reamains unable to meddle in the affair, all the three, whatever you want) it's a game changer for the whole continent. Bolívar knew it, and as soon as he had news of the treaty wrote to San Martín sharing his worries about the consequences in the rest of the continent. In his own words (sorry, I have not the direct quote at hand, so you have to trust my memory) a royalist Mexico would have a more cohesive government, more stability and thus would be threat to Gran Colombia. He knew they were creating a new legitimacy, but that in the mindsets the old legitimacy was still very strong. Not to mention that Peruvians most probably would want also something like that (though at this point there is not much that Spain could do there directly, it could be a source of unrest and an added difficulty to the separatist campaings there.) and it even could tempt sectors of the cocieties inside the already independent territories. So, my bet is that facing this threat, Bolívar and co decide they have to do something to counter it. A new political approach, more prone to devolution (not sure if Bolívar would be able to accept a confederal project, however, but at least a federal one) an effort to attract wills by diplomatic means instead by force, peace negotiations with Spain while the boogeyman of the royalist presence up the north is useful to keep the attentions outside instead inside...