Relying on the creeps to cap flags would seriously change the momentum of flag capturing, though. It may not be bad to do that, but it does need to be considered, especially as flags start meaning more when they become the source for creep upgrades.
The overall flow of the back and forth needs to be visualized, and any changes you make need to be viewed within that lens. If all progression requires the use of creeps, surgical strikes become relatively difficult. A push has a very different feel in terms of pacing than something that's more uniquely hero based. I think it may be a better use of flags to decouple them more from creeps rather than tying them closer, as they're more easily adapted to a soft target. This means you'd have lots of flags that don't have portals or significant defenses tied to them, but act only as resource points for the hero units to fight over. Simply making early creep pushes more viable early game (which can be accomplished by a little stat modification) if heroes aren't defending towers while doing the above generates an interesting choice. If you attempt to go after flags, you're no longer defending your towers, if you attempt to defend your towers, you've less access to resources.
One thing that does need to be looked at though, is perhaps adding more in the way of upkeep and less in the way of upgrades. Having a continual burn of flag generated resource instead of a one time upgrade cost to increase the power of your creeps would make resource denial a viable strategy and add a lot of depth in terms of tactics all by itself. It also allows greater back and forth; if one team is winning, a blow to their resources can cause them to lose some of the advantages that they've built up and allow for a comeback from the other side.
Edit: To explain that last bit a little more: Coupling resource advantages to "soft" targets rather than something like tower destruction has the benefit of changing the dynamic away from a slippery slope situation, at least partially. If resources are granted for getting closer to the win condition - every tower you take down is that much closer to winning - then you end up with the better team having even more of an advantage, and the losing team has that much harder of a time. If you decouple these things, so that softer easily raided points provide a stronger resource benefit than whether or not you're moving toward the destruction of the enemy base, it's easier for the losing team to recover. That's important for a sense of back and forth, and makes it tenser up to the end. There are more points of weakness to worry about, and you need to be watching out for an upset.
