Yes, by making a caster level check and meeting some requirements
The relevant rules are all in the Magic Items - Scrolls section of the DMG. Here's a copy from the SRD. There are two steps:
Decipher the Writing
The writing on a scroll must be deciphered before a character can use
it or know exactly what spell it contains. This requires a read magic
spell or a successful Spellcraft check (DC 20 + spell level).
Deciphering a scroll to determine its contents does not activate its
magic unless it is a specially prepared cursed scroll. A character can
decipher the writing on a scroll in advance so that he or she can
proceed directly to the next step when the time comes to use the
scroll.
Read Magic is a level 0 Cleric spell, so your player can prepare and cast it to perform this step. They could also use the Spellcraft skill instead, but a DC 23 Spellcraft check can be difficult for a level 2 Cleric to make.
Activate the Spell
To have any chance of activating a scroll spell, the scroll user must
meet the following requirements.
The spell must be of the correct type (arcane or divine). Arcane spellcasters (wizards, sorcerers, and bards) can only use scrolls
containing arcane spells, and divine spellcasters (clerics, druids,
paladins, and rangers) can only use scrolls containing divine spells.
(The type of scroll a character creates is also determined by his or
her class.)
Assuming you're giving out a Divine scroll, this is no problem.
The user must have the spell on his or her class list.
Clerics have Remove Disease on their spell list, so this is no problem.
The user must have the requisite ability score.
Remove Disease is a third level Cleric spell, so your Cleric requires 13 Wisdom to meet this requirement.
If the user meets all the requirements noted above, and her caster
level is at least equal to the spell’s caster level, she can
automatically activate the spell without a check. If she meets all
three requirements but her own caster level is lower than the scroll
spell’s caster level, then she has to make a caster level check (DC =
scroll’s caster level + 1) to cast the spell successfully. If she
fails, she must make a DC 5 Wisdom check to avoid a mishap (see Scroll
Mishaps, below). A natural roll of 1 always fails, whatever the
modifiers.
Being a third level spell, the caster level requirement is 5. You can tell that because it's a third level spell, and Clerics get third level spells at level 5.
Your Cleric is likely a level 2 Cleric, thus has a caster level of 2. That isn't sufficient to meet this requirement, so your Cleric will have to make a caster level check of DC 6 (5 + 1). A caster level check is 1d20 + caster level, or 1d20+2. Only needing a a total of 6, a 4 or better on the dice will let your Cleric cast the spell. Those are good odds.
At Cleric level 5, your player can cast the scroll without having to make the check.
If your Cleric doesn't meet the other requirements, or someone else wants to use the scroll, they have to use Use Magic Device instead.
You're misusing the guidelines.
First, let's take a look at what the Pathfinder Magic Item Gold Piece Values section has to say on this issue. Turns out, it is specifically addressed.
The correct way to price an item is by comparing its abilities to similar items (see Magic Item Gold Piece Values), and only if there are no similar items should you use the pricing formulas to determine an approximate price for the item. If you discover a loophole that allows an item to have an ability for a much lower price than is given for a comparable item, the GM should require using the price of the item, as that is the standard cost for such an effect. Most of these loopholes stem from trying to get unlimited uses per day of a spell effect from the "command word" or "use-activated or continuous" lines of Table: Estimating Magic Item Gold Piece Values.
Emphasis mine. It then goes on to take Mage Armor as an example of this:
Patrick's wizard wants to create bracers with a continuous mage armor ability, granting the wearer a +4 armor bonus to AC. The formula indicates this would cost 2,000 gp (spell level 1, caster level 1). Jessica reminds him that bracers of armor +4 are priced at 16,000 gp and Patrick's bracers should have that price as well. Patrick agrees, and because he only has 2,000 gp to spend, he decides to spend 1,000 gp of that to craft bracers of armor +1 using the standard bracer prices.
So yes, your Amulet of Mage Armor and Shield is a textbook example of the guidelines gone bad.
This is understandable. The guidelines are famously weak, often breaking with casual use, as you have encountered. This precise case, however, was anticipated and addressed.
Best Answer
Yes, but with contingencies...
So, first off, I will say that these will most definitely stay relevant. As the rogue, when you get into higher levels the ONLY way you stay relevant is doing the stuff other party members can't. Pathfinder isn't as bad as its DnD 3.5e roots in this line, but Rogues are still far less powerful than many other classes in a "traditional power" sense.
That said, your goal, again, is to do what they can't. What you do best is take out people that would pose serious problems. You are the master of 1v1 stealth attacks, the "getting the final killing hit in a hard battle" person.
For that, these abilities do stay relevant. Ranged Touch SA, for example, are drastically underestimated, but especially vs tanky opponents they can be a huge boon because you can bypass normal defenses.
As a Rogue, you want to aim towards "toolboxing" yourself a bit. Toolboxing refers to the idea of having an good answer to many problems as opposed to a few ridiculously powerful answers to a few problems. These things you are looking at help you do just that.
As a personal note, yes...you will lose straight up melee power and SA damage of dual-wielding rogues. That's fine, though...that isn't your gimmick, and in my opinion it is a waste of rogue potential. You, however, are swapping that pure damage for a rather nice set of utilities that enable you to penetrate defenses, deal damage, stay alive, etc.
Also remember that higher-level encounters will generally go quickly with a good party, so things that can't be used often have more weight because you don't need to worry about 5 rounds of trying to deal with a random enemy like you do at lower levels.
From the perspective of a person who enjoys Pathfinder rogues and rogue-likes, I can say you definitely are making a good choice. Just make sure you play to these strengths and don't go after the same format as those stereotypical two-dagger users. ;)