If you give them humanoid hit dice, you really ought to up their total ECL. Changing their ECL to a total of +4, with 2 humanoid hit dice and a +2 Level Adjustment, would lessen the impact.
Also, Svirfneblin don't really have it all that tough. They're Small, get +2 Dexterity and Wisdom, get a +4 dodge bonus against everything, get a +2 on all saving throws, and get Spell Resistance of 11 + class levels. So a Svirfneblin with 1 class level (wizard, rogue, or whatever you like) has SR 12, and lots of other defensive benefits. Sure they suffer -2 Strength and -4 Charisma, but so what?
Wizard is a really, really suboptimal choice for Deep Gnomes, anyway. I understand it from a flavor point of view, but otherwise? Ack, so many drawbacks. No Intelligence bonus despite the +3 Level Adjustment. 3 levels worth of spellcasting essentially lost (and 3 levels worth of familiar improvements), at least until you reach epic levels. No other racial bonuses to feats or spellcasting. No Constitution bonus like Rock Gnomes get. Gonna really hurt in the Hit Points and spellcasting departments. Deep Gnomes make slightly better clerics, druids, and rangers than they do arcane casters (albeit thematically tougher to justify).
Make it a Svirfneblin Rogue 1 (ECL 4), with 20 Dexterity and 18 Constitution (or 20 Dexterity and 14 Constitution, depending on how you determine ability scores or what you rolled). Let's say you end up with Strength 8, Dexterity 20, Constitution 14, Wisdom 12, and Charisma 4 (you'll be one butt-ugly, rude, smelly, sarcastic, snarky gnome! Love it!). As a 1st-level Rogue, you could be wearing Masterwork Studded Leather Armor (+3 AC), carrying a Heavy Shield (+2 AC, take the Shield Proficiency feat to use well), and getting another +5 AC from Dexterity, +4 AC from dodge as a Svirfneblin, and +1 AC for being Small in size.
You'll be 4th-level equivalent with 8 Hit Points and AC 25, as well as a total Fortitude save of +4, Reflex of +9, and Will of +3, plus a Spell Resistance of 12. You'll be really tough to hit, really tough to blast with magic, and really sneaky (since Deep Gnomes get +4 Hide for being Small, and +2 racial that becomes +4 in dark underground places). Especially with the +5 bonus on Hide and Move Silently from Dexterity, the Nondetection benefit fo Deep Gnomes, the Change Self (Disguise Self in 3.5) ability of Deep Gnomes, and the fact that Svirfneblin can use Blindness and Blur once a day, so they can make themselves even harder to hit as well as give an opponent difficulty in finding or hitting them at all. You'd rely on Sneak Attack for damage (often through flanking, but as a side-benefit, your Blindness ability as a Deep Gnome will make you effectively invisible to whatever opponent you use it on, so you can sneak-attack away!).
For attack bonuses, you'll have +1 size (balanced by the -1 Strength penalty in melee), and then rely on blinding enemies, flanking, and such to make it easier to hit. Once you gain another feat, it'd be Weapon Finesse so you could jack up your melee attack bonus with a dagger or short sword. Even before that, your ranged attack bonus will rock (+5 Dex, +1 size, and any enhancement or masterwork bonus from the weapon; you'll have plenty of cash probably to get a +1 weapon most likely).
(a note: I'm referring to my 3.0 Forgotten Realms Campaign Setting book for Deep Gnome stats; may've been slightly tweaked in the 3.5 Player's Guide to Faerun)