What if your competitor came up with the same algorithm (or very similar) and performs as well both in time and space complexity... and all of this on their own, without actually taking a peek at your code. In that case would you go after them and sue them?
I imagine we would, simply because we can; we're a commercial entity after all. Personally (and I'm not representing my company here) I don't think that's a good thing; if they could prove that they independently reached the same results without using any of our research or work (or we couldn't prove the contrary), they should be protected. That's not the case though at the moment unfortunately.
I agree, its not the same case. The problem might be in 15 years from now, your algorithm might just become a very natural way to solve that specific problem and at that point how your company plays this out matters. My guess is the companies that are in the business of making, creating, producing and then selling software themselves, will be ok with it. These trolls like Lodsys try to neither produce nor create. A very important rule for the any type of patent should enforce "active" product in use/development.
Sadly, it might never happen.