For me the "building game" is less interesting because it requires less action from me. There is planning and decision making but very little interraction between me and the game. Warfare, on the other hand, is interesting because there is so much more to do. You still have to build infrastructure, maintain your economy and deal with diplomacy just like a builder does but at the same time you get to move a lot of units around, attack cities and thwart your opponents attacks.
Maybe all you need to do is make the "builder's game" more interractive. For example, why is there only one generic worker? If there was only one generic "army" unit war would probably be no more interesting. It wouldn't take much to make different types of workers such as "farmers" who can only build farms and pastures or lumberjacks who can only clear forest and jungle tiles, maybe even an option between slow moving workers with higher work rates and faster moving workers with lower work rates. If you needed more workers to accomplish the same tasks it would require more interraction, a few more decisions and some new limitations to overcome.
Other possibilities would be improvements that don't auto-upgrade. An example of this could be farms that initially don't spread irrigation but when you discover irrigation you can build an irrigated farm which produces more food and spreads irrigation. The same could be done with mines, windmills, lumbermills and watermills. Perhaps these wouldn't be buildable by the same worker you've been using all game so you'd have to upgrade them just like you do your military units.
Getting away from units you have the cities themselves. Some changes to allow larger cities without making them too much more powerful would give you more options with specialists (which could also be less potent). Building limits per city would give you more to consider rather than simply building everything that is available and buildings that cancelled out or prevented the construction of other buildings would create more "strategic" options.
You can also "cripple" conquest by doing something as simple as increasing the number of national wonders and using some of them to replace world wonders. If everybody can create their own Stonehenge then capturing or destroying an opposing civ's city with Stonehenge has less of a long term impact on the game and no impact on other civs.
A few relatively minor changes to the AI leaders can go a long way as well. For example you could increase the negative effect of declaring war on a civ and decrease the negative effect of trading with an enemy. There are a lot of small changes here than can make warfare much more of a strain on relations than anything else and if this would cause more AI players to cut off current deals with you or declare war on you it can make it substantially more difficult to wage war.
Just some random thoughts that wouldn't require much more than some xml changes