I've never dealt with that short of a connection, but that would definitely make me nervous. 25 minutes is a very short connection, and any delay at all would make you miss it. You'll need everything to be perfectly on time with the first flight to have a chance of making it. Even an hour can be a tight connection, but it's better.
Even if you pay for EBCI, I definitely wouldn't count on being able to benefit from it at that point. Boarding will likely (but not necessarily) have already begun once you land, and you'll need to remember that the 25 minute connection includes the time it takes to get off the plane in HOU, get to the next gate, and board. Your chances of making the flight at all aren't overly great, so the chances of making it for EBCI boarding are even slimmer.
I would be a bit less leery of it if you didn't have specific needs, such as a window seat for your 2-year-old. If it was a bunch of adults who are able to run from gate to gate and take whichever seat they can get, it may be a different story.
I think you also need to consider what time of day you're flying and where you're flying from. If it's the first flight in the morning, you're less likely to have delays and more likely to be able to make it. If your city's airport is smaller or generally not prone to delays, it may also be more feasible. You'll also want to consider how large Southwest's operations are in Houston and how far apart the gates would be in the worst case scenario.
Although airlines won't hold a plane for someone who is late getting to the airport, they will sometimes hold a plane for a couple minutes if they know a group is coming in off of a connecting flight. There's no guarantee of this, however, so I think I'd book the flight connecting through Midway just to be a bit safer (as long as the prices, times, etc. are equally good).