This answer is derived from Thornton's War in Atlantic Africa, 1500-1700.
Firstly, the nature of war in Angola limited the effects of one single battle: Kongo lost at Mbwila but then emerged victorious at Kitombo in 1670. Given that cavalry could not be used in the disease-ridden region, there was no way to chase down routing armies.
Portugal controlled the major rivers (Kwanza, Lukala) and the coast, so victorious Kongolese armies would have run against those barriers at some point.
Native Angolan defence focused on fortified hilltop villages which served as mustering-points, supply stores as well as places of refuge: these had to be sieged down in order to gain any control over the land. Slash-and-burn agriculture made native populations transient and therefore 'living off the land' was rarely an option. All these, coupled up with long distances, made logistics key to conquest in Angola... and 17thC Portugal never invested the sort of time or resources required for such conquest. Nor did they want to - their aims in Angola were to maintain their trade monopoly against the Dutch, for which loose vassalage treaties with native kings would suffice.
Secondly, 'native Kongolese' is far too broad a term considering the political diversity of the region. There were rival kingdoms such as Ndongo, Matamba or the 18thC Lunda Empire, and many smaller ones who formed the larger portion of 'Portuguese' armies.
More dangerously, there were also roving Imbangala armies, fuelled by the slave trade, who were more than capable of wrecking native kingdoms (Benguela in the 16thC). None of these wanted Kongo to dominate the region: neighbors, not colonial armies, were the main constraint on Kongolese expansion/development during this period.
Thirdly, Kongo's political structure, not defeat at Mbwila, was the cause behind the country's decline. Kongo's nobility were placed in charge of provincial armies. While mobilization was the central government's prerogative, and Kongolese nobles could and were moved around the country (unlike in Ndongo), the fact is that the level of centralization in Kongo was still not terribly strong.
It was not so difficult for this political system to transition, during the 1660s civil war, into semi-autonomous provinces, each under the rule of a pretender king. Perhaps Mbwila accelerated this trend, but the threat was always there and maybe some other event would have triggered it had Mbwila not occurred.
Lastly, it's not clear that one can draw a line of causation from Mbwila to the ultimate subjugation of Angola under Portugal. We've already seen that 'vassalage' was largely a trade-based relationship with some military obligations in times of war. Neither native kingdoms nor colonial Angola possessed the force to overpower the other, and leaders on both sides knew it. Mbwila perhaps began the process of a somewhat-unified Kongo into a barely-unified Kongo, but for 17thC Portugal that merely meant more 'vassal' treaties to be negotiated, more political relationships to manage - they certainly did not see it as a 'green light' for colonial expansion.
In fact, that sort of fighting only distracted leaders from their real goals, which were to benefit from the slave-gun trade and to skirmish against the political rivals of the day. The two were, of course, not entirely separate motivations.
TL;DR - Victory in Angolan wars was rarely decided by battle; Kongo's main threats came not from Portugal, but from rebels and neighbors; Mbwila likely contributed to Kongo's decentralization but did not cause it; and it's anachronistic to draw a line from Mbwila to the ultimate Portuguese colonization.