Could World Cup expansion to 48 teams actually end up hurting South American national teams?

Over the last 15-20 years we have seen a significant improvement in the quality level of middle-tier South American sides. Teams that would have previously been routed by European teams in the group stage of the WC, or not even qualified at all, have found themselves advancing deeper into the tournament. Examples include the following:

Ecuador in 2006 making it to the knock-out stage in Europe
Paraguay in 2010 reaching the quarters and giving Spain their toughest challenge
Colombia in 2014 also reaching the quarters
Chile excelling in 2010 and 2014

Why is that? One big reason seems to be the grueling and highly competitive qualifying format now used in South America. Until 1996, South American teams played just a few matches (sometimes as few as just four matches in groups of three teams). This system created large time gaps between meaningful matches, which prevented teams from coalescing they way that European teams could in their more crowded UEFA qualification tournament.

The current system of having all ten South American teams playing each other on a round-robin home-and-away basis results in a grueling 18 game schedule that is spread out over two years. It is this highly demanding qualification structure that is credited with raising the level of play of middle-tier teams in the region.

When the World Cup expands to 48 teams it is likely that South America will receive two more automatic qualifying spots. This would water down the 18-match tournament as the number of qualifying spots would increase from the 4.5 places to 6.5 places. Instead of fighting tooth-and-nail to the bitter end, many teams would clinch advancement at a much earlier time. This could really kill the competitive edge as only 3.5 teams from the region would end up being eliminated.

Should the qualifying tournament be restructured in some innovative way? Perhaps CONMEBOL and CONCACAF could merge their qualifying tournaments? What solutions would you like to see implemented to this potential problem?