I think each group needs to determine for themselves what is (or is not) fun. If a rule (or class, feat, spell, etc.) inhibits the player's (and the group's) enjoyment then that group ought to determine whether they should fix, replace, or eliminate said rule.
If the OP finds that this change to the rules makes for a more enjoyable experience for his player and his group, then, by all means, implement the change. If not, then don't. I am not sure increasing the fighter's damage capacity would be of any real benefit in the campaigns that I run, however. My campaigns tend to feature more lower-CR creatures to make up the EL rather than one or two, higher-CR creatures. As such, I think that the fighter's increase in damage would often result in the fighter doing excess damage, thereby negating any actual benefit to the increased damage capacity.
Re: Balance and 3.5 - I have found that I most enjoy the game when all characters are Tier 2, 3, or 4. For me, balancing the fighter with the wizard is not what I am interested in. Rather, I would prefer to balance the fighter against the rest of Tier 4 and the wizard against the rest of Tier 2. That brings their power level more in line with my -- and my group's -- comfort zone.