Sacrificing 1 or 2 levels of spell casting is a default cost for any something/spellcaster prestige class. If you have full spellcasting ability AND other class's ability (rogue abilities, full BAB, etc.), that makes your character simply stronger than as straight spell caster and it never happens without using UA rules which meant not to be balanced against usual characters.
By the way, I actually played Shadowbane Stalker in a campaign and he was a super problem solver. Divine Insight was so great when combined with rogue abilities. You found DC 35 magical trap? Disable device with +15 skill boost. You must tumble past an opponent square and the DC for the tumble check is too high? Trigger Divine Insight.
The alternative to this could be Rogue or Scout 1-2/Cleric forever. This way, unlike Shadowbane Stalker build, you can keep having reasonably high Turn Undead ability (especially if your play group is using alternative rule in Complete Divine). Be a Human and take Able Learner feat from Races of Destiny. Now you can buy Rogue class skills at 1 skill point per level even when leveling up as a cleric. If you invest 14 for your int, you can get 5 skill points per level and thus can easily max out Disable Device and Search, then take other skills necessary at reasonable level. Again, use Divine Insight whenever you need to beat high DC skill checks.