Hearing loss from shooting indoors in a home defense situation is a concern of mine as well.
As others have said, when your life or the lives of your loved ones are at risk, the cost-benefit analysis of suffering lifelong hearing loss versus being killed is a no-brainer: everyone would rather live the rest of their life with hearing loss than not live at all. That said, I still think it's prudent to consider ways you might reduce the damage.
I keep a set of ear plugs close to my home defense shotgun. I'm not sure I would have the presence of mind to put them on, especially in the heat of the moment when I'm relying on my hearing to detect where the intruders are and what they're doing, but at least having them nearby gives me the option of using them if I can.
I also selected my home defense firearm, a Mossberg HS410, with the thought of minimizing hearing loss and flash/bang disorientation to the greatest extent possible while still packing enough power to put down an intruder. For that reason, and others, I chose the Mossberg HS410 shotgun as my primary home defense firearm.
A 410 shotgun with an 18" barrel fired indoors is by no means quiet, but at 156.30db it's undeniably less loud than most any other firearm:
http://keepandbeararms.com/information/XcIBViewItem.asp?ID=2052
Table 2. SHOTGUN NOISE DATA (DECIBEL AVERAGES)
.410 Bore 28" barrel 150dB
26" barrel 150.25dB
18 " barrel 156.30dB
20 Gauge 28" barrel 152.50dB
22" barrel 154.75dB
12 Gauge 28" barrel 151.50dB
26" barrel 156.10dB
18 " barrel 161.50dB
CENTERFIRE RIFLE DATA
.223, 55GR. Commercial load 18 " barrel 155.5dB
.243 in 22" barrel 155.9dB
.30-30 in 20" barrel 156.0dB
7mm Magnum in 20" barrel 157.5dB
.308 in 24" barrel 156.2dB
.30-06 in 24" barrel 158.5dB
.30-06 in 18 " barrel 163.2dB
.375 18" barrel with muzzle brake 170 dB
CENTERFIRE PISTOL DATA
.25 ACP 155.0 dB
.32 LONG 152.4 dB
.32 ACP 153.5 dB
.380 157.7 dB
9mm 159.8 dB
.38 S&W 153.5 dB
.38 Spl 156.3 dB
.357 Magnum 164.3 dB
.41 Magnum 163.2 dB
.44 Spl 155.9 dB
.45 ACP 157.0 dB
.45 COLT 154.7 dB
I hope I never have to use my HS410 in a home defense situation. But if I do have to use it, I hope that the reduced recoil and lesser flash/bang will result in a less disorienting first shot that will allow me to fire off effective 2nd and 3rd shots, if necessary.
Just my two-cents.