How I would handle this would depend upon the performance of the ecommerce website and which entrance paths via the website convert higher.
You could easily instruct search engines not to index the search results page by adding the following in your robots.txt:-
Disallow: /search.php?search=*
But is there a real likelihood of duplicate matching content with your actual category pages? It's unlikely in all honesty - but depending on your website content and product range, I suppose possible.
If many visits to your website arrive via indexed search result pages, I would be inclined to leave them indexed however and implement measures to ensure that they won't be flagged as duplicate content.
Ways to handle this depend on your ecommerce provider and it's capabilities sometimes but more often that not, is just a case of ensuring there is plenty of unique content on your category pages (as there should be) and there is no chance of other pages of your website hindering their ranking potential then.