The crux of the Conflict/Morality mechanic is that the PC has to be faced with situations that have the potential to earn them Conflict points in the first place, and not just those from making use of dark side pips on their Force dice when activating powers.
Frankly it's up to the GM to give the players difficult situations where the easier paths to solve a dilemma will generate Conflict points, because they are the "quick and easy" solution. If the GM doesn't do that, then yes a player will be able to rise to Light Side Paragon status pretty easily, because there hasn't been anything to challenge that progression. It's pretty easy for the average person to walk a quarter mile when it's a flat, even surface, the weather is bright, sunny, and pleasantly warm, and you're properly feed. It's a whole 'nother story to walk a quarter mile when it's the middle of a winter night in a freezing downpour in an area you don't know with uneven terrain and there's bear traps scattered between you and your destination.
Resorting to violence as the first response to a problem is worth Conflict, because you didn't explore any alternatives to fighting and went straight to kicking your current opponent's hindquarters. There might be some leeway if the opponents attacked you directly before you could explore an alternate option, but even if your first response is "grab my weapon and start blasting/slicing," that's probably worth a point of Conflict. You could fully attempt to scare off a lesser threat, like a pack of street toughs thru a Coercion check, and while that's probably worth a point of Conflict itself, it's certainly more merciful than chopping them up with a lightsaber simply for crossing your path at a bad time. A GM could potentially award Conflict for using lethal force instead of stun damage if the option's available, but I'd not suggest doing this on a recurring basis; after all, a weapon's a weapon, and part of the reason the classic Jedi carried only a inherently lethal lightsaber was to reinforce that a Jedi's first response shouldn't be "draw my lightsaber."
If you need to get through a door, and your first response is to rip it out of its moorings via the Force without seeing if there's other means to get through the door, namely picking/slicing the lock or seeking another way in, that's worth a substantial amount of Conflict because your first response was unnecessary property damage. Qui-Gon in TPM probably got a few Conflict points for trying to carve his way through the doors to the bridge of the Trade Federation ship, but the player accepted that it needed to be done and figured that as long as he doesn't make a routine habit of that kind of behavior he should be okay in terms of him remaining a Light Side Paragon.
Torture, both mental and especially physical, is going to generate lots of Conflict because you're inflicting unnecessary harm on somebody that's pretty much at your mercy. Same will killing an opponent you've already defeated, since they're no longer a threat to you.
The Conflict/Morality system is no more inherently flawed than Obligation or Duty are, and I've heard of games where the GM never gave his EotE players the opportunity to reduce their Obligations, something the rulebook says the GM should offer, either as an adventure reward in lieu of credits or even as the major reward of an adventure. And until Andy Fischer made a guest appearance on the Order 66 podcast to suggest the average Duty award per session should be around 5 points, there were a number of GMs that were only handing out 1 or 2 Duty points per session, making for a very anemic progression to the group's next Contribution Rank.
If anything, the core "flaw" is that most players who are familiar with the Star Wars universe, when playing Force users if not actual aspiring Jedi, are going to take their cues on how to act from the Jedi we see on the screen, most notably Obi-Wan and RotJ!Luke as general examples of "What Would a Proper Jedi Knight Do?" and will thus act far more noble than they might were they playing a smuggler or bounty hunter. Thus, they'll see situations that might generate Conflict and try to avoid them simply because "it's what a Jedi would do." And if the players are going to act like good guys instead of a pack of blood-crazed murder hobos, then I'd say they should receive a benefit for not stooping to their darker urges.
That is a great point - the Morality system actually encourages and rewards good characters without unduly punishing PCs that fall to the dark side.
Also, since Morality is a "core book" mechanic and optional it allows GMs to run a game where the force users have Morality, while the non-force users use Duty/Obligation which recreates the feel of the movies and EU that force users are particularly susceptible to their darker impulses and the amplified impact this can have on external events.